<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2022-07-28T15:59:06.3252+00:00 -->
<!-- Copyright (c) 2022 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<xsd:schema targetNamespace="http://www.ultragenyx.com/20220630" attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:country="http://xbrl.sec.gov/country/2021" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2020-01-21" xmlns:enum2="http://xbrl.org/2020/extensible-enumerations-2.0" xmlns:srt="http://fasb.org/srt/2021-01-31" xmlns:rare="http://www.ultragenyx.com/20220630" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:us-gaap="http://fasb.org/us-gaap/2021-01-31" xmlns:dei="http://xbrl.sec.gov/dei/2021q4" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xlink="http://www.w3.org/1999/xlink">
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/instance"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/linkbase"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" namespace="http://xbrl.org/2005/xbrldt"/>
  <xsd:import schemaLocation="https://xbrl.sec.gov/country/2021/country-2021.xsd" namespace="http://xbrl.sec.gov/country/2021"/>
  <xsd:import schemaLocation="https://xbrl.fasb.org/srt/2021/elts/srt-2021-01-31.xsd" namespace="http://fasb.org/srt/2021-01-31"/>
  <xsd:import schemaLocation="https://www.xbrl.org/2020/extensible-enumerations-2.0.xsd" namespace="http://xbrl.org/2020/extensible-enumerations-2.0"/>
  <xsd:import schemaLocation="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd" namespace="http://fasb.org/us-gaap/2021-01-31"/>
  <xsd:import schemaLocation="https://xbrl.sec.gov/dei/2021q4/dei-2021q4.xsd" namespace="http://xbrl.sec.gov/dei/2021q4"/>
  <xsd:import schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd" namespace="http://www.xbrl.org/dtr/type/2020-01-21"/>
  <xsd:annotation>
    <xsd:appinfo>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="rare-20220630_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:title="Labels link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="rare-20220630_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:title="Presentation link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="rare-20220630_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:title="Definition link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="rare-20220630_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:title="Calculation link" xlink:type="simple"/>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DocumentDocumentAndEntityInformation" id="Role_DocumentDocumentAndEntityInformation">
        <link:definition>100000 - Document - Document and Entity Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_StatementCONDENSEDCONSOLIDATEDBALANCESHEETS" id="Role_StatementCONDENSEDCONSOLIDATEDBALANCESHEETS">
        <link:definition>100010 - Statement - CONDENSED CONSOLIDATED BALANCE SHEETS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_StatementCONDENSEDCONSOLIDATEDBALANCESHEETSParenthetical" id="Role_StatementCONDENSEDCONSOLIDATEDBALANCESHEETSParenthetical">
        <link:definition>100020 - Statement - CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFOPERATIONSUnaudited" id="Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFOPERATIONSUnaudited">
        <link:definition>100030 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/StatementCondensedConsolidatedStatementsOfComprehensiveLossUnaudited" id="StatementCondensedConsolidatedStatementsOfComprehensiveLossUnaudited">
        <link:definition>100040 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFSTOCKHOLDERSEQUITYUnaudited" id="Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFSTOCKHOLDERSEQUITYUnaudited">
        <link:definition>100050 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFCASHFLOWSUnaudited" id="Role_StatementCONDENSEDCONSOLIDATEDSTATEMENTSOFCASHFLOWSUnaudited">
        <link:definition>100060 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureOrganization" id="Role_DisclosureOrganization">
        <link:definition>100070 - Disclosure - Organization</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPolicies" id="Role_DisclosureSummaryOfSignificantAccountingPolicies">
        <link:definition>100080 - Disclosure - Summary of Significant Accounting Policies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureFinancialInstruments" id="Role_DisclosureFinancialInstruments">
        <link:definition>100090 - Disclosure - Financial Instruments</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponents" id="Role_DisclosureBalanceSheetComponents">
        <link:definition>100100 - Disclosure - Balance Sheet Components</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureRevenue" id="Role_DisclosureRevenue">
        <link:definition>100110 - Disclosure - Revenue</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreements" id="Role_DisclosureLicenseAndResearchAgreements">
        <link:definition>100120 - Disclosure - License and Research Agreements</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLiabilityRelatedToSaleOfFutureRoyalties" id="Role_DisclosureLiabilityRelatedToSaleOfFutureRoyalties">
        <link:definition>100130 - Disclosure - Liability Related to the Sale of Future Royalties</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureStockBasedAwards" id="Role_DisclosureStockBasedAwards">
        <link:definition>100140 - Disclosure - Stock-Based Awards</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureNetLossPerShare1" id="DisclosureNetLossPerShare1">
        <link:definition>100150 - Disclosure - Net Loss Per Share</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureEquityTransactions" id="Role_DisclosureEquityTransactions">
        <link:definition>100160 - Disclosure - Equity Transactions</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureAccumulatedOtherComprehensiveLoss" id="DisclosureAccumulatedOtherComprehensiveLoss">
        <link:definition>100170 - Disclosure - Accumulated Other Comprehensive Loss</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureSubsequentEvents" id="DisclosureSubsequentEvents">
        <link:definition>100180 - Disclosure - Subsequent Events</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" id="Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies">
        <link:definition>100190 - Disclosure - Summary of Significant Accounting Policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesTables" id="Role_DisclosureSummaryOfSignificantAccountingPoliciesTables">
        <link:definition>100200 - Disclosure - Summary of Significant Accounting Policies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureFinancialInstrumentsTables" id="Role_DisclosureFinancialInstrumentsTables">
        <link:definition>100210 - Disclosure - Financial Instruments (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponentsTables" id="Role_DisclosureBalanceSheetComponentsTables">
        <link:definition>100220 - Disclosure - Balance Sheet Components (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureRevenueTables" id="Role_DisclosureRevenueTables">
        <link:definition>100230 - Disclosure - Revenue (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreementsTables" id="Role_DisclosureLicenseAndResearchAgreementsTables">
        <link:definition>100240 - Disclosure - License and Research Agreements (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesTables" id="Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesTables">
        <link:definition>100250 - Disclosure - Liability Related to the Sale of Future Royalties (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureStockBasedAwardsTables" id="Role_DisclosureStockBasedAwardsTables">
        <link:definition>100260 - Disclosure - Stock-Based Awards (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureNetLossPerShareTables" id="DisclosureNetLossPerShareTables">
        <link:definition>100270 - Disclosure - Net Loss Per Share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureAccumulatedOtherComprehensiveLossTables" id="DisclosureAccumulatedOtherComprehensiveLossTables">
        <link:definition>100280 - Disclosure - Accumulated Other Comprehensive Loss (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureOrganizationAdditionalInformationDetails" id="Role_DisclosureOrganizationAdditionalInformationDetails">
        <link:definition>100290 - Disclosure - Organization - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfReconciliationOfCashCashEquivalentsAndRestrictedCashDetails" id="Role_DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfReconciliationOfCashCashEquivalentsAndRestrictedCashDetails">
        <link:definition>100300 - Disclosure - Summary of Significant Accounting Policies - Summary of Reconciliation of Cash, Cash Equivalents and Restricted Cash (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureFinancialInstrumentsSummaryOfFinancialAssetsMeasuredOnRecurringBasisDetails" id="Role_DisclosureFinancialInstrumentsSummaryOfFinancialAssetsMeasuredOnRecurringBasisDetails">
        <link:definition>100310 - Disclosure - Financial Instruments - Summary of Financial Assets Measured on Recurring Basis (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponentsSummaryOfCashEquivalentsAndInvestmentsClassifiedAsAvailableForSaleSecuritiesDetails" id="Role_DisclosureBalanceSheetComponentsSummaryOfCashEquivalentsAndInvestmentsClassifiedAsAvailableForSaleSecuritiesDetails">
        <link:definition>100320 - Disclosure - Balance Sheet Components - Summary of Cash Equivalents and Investments Classified as Available For Sale Securities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponentsAdditionalInformationDetails" id="Role_DisclosureBalanceSheetComponentsAdditionalInformationDetails">
        <link:definition>100330 - Disclosure - Balance Sheet Components - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponentsSummaryOfInventoryDetails" id="Role_DisclosureBalanceSheetComponentsSummaryOfInventoryDetails">
        <link:definition>100340 - Disclosure - Balance Sheet Components - Summary of Inventory (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureBalanceSheetComponentsAccruedLiabilitiesDetails" id="Role_DisclosureBalanceSheetComponentsAccruedLiabilitiesDetails">
        <link:definition>100350 - Disclosure - Balance Sheet Components - Accrued Liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureRevenueSummaryOfDisaggregationOfTotalRevenuesFromCustomersDetails" id="Role_DisclosureRevenueSummaryOfDisaggregationOfTotalRevenuesFromCustomersDetails">
        <link:definition>100360 - Disclosure - Revenue - Summary of Disaggregation of Total Revenues from Customers (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureRevenueSummaryOfDisaggregationOfTotalRevenuesDetails" id="Role_DisclosureRevenueSummaryOfDisaggregationOfTotalRevenuesDetails">
        <link:definition>100370 - Disclosure - Revenue - Summary of Disaggregation of Total Revenues (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureRevenueSummaryOfChangesInContractLiabilitiesDetails" id="DisclosureRevenueSummaryOfChangesInContractLiabilitiesDetails">
        <link:definition>100380 - Disclosure - Revenue - Summary of Changes in Contract Liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureRevenueAdditionalInformationDetails" id="Role_DisclosureRevenueAdditionalInformationDetails">
        <link:definition>100390 - Disclosure - Revenue - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreementsAdditionalInformationDetails" id="Role_DisclosureLicenseAndResearchAgreementsAdditionalInformationDetails">
        <link:definition>100400 - Disclosure - License and Research Agreements - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreementsShareOfCollaborationAndRoyaltyRevenueRelatedToCrysvitaDetails" id="Role_DisclosureLicenseAndResearchAgreementsShareOfCollaborationAndRoyaltyRevenueRelatedToCrysvitaDetails">
        <link:definition>100410 - Disclosure - License and Research Agreements - Share of Collaboration and Royalty Revenue Related to Crysvita (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreementsScheduleOfCostSharingPaymentsDetails" id="Role_DisclosureLicenseAndResearchAgreementsScheduleOfCostSharingPaymentsDetails">
        <link:definition>100420 - Disclosure - License and Research Agreements - Schedule of Cost Sharing Payments (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLicenseAndResearchAgreementsScheduleOfChangesInFairValueOfEquityInvestmentDetails" id="Role_DisclosureLicenseAndResearchAgreementsScheduleOfChangesInFairValueOfEquityInvestmentDetails">
        <link:definition>100430 - Disclosure - License and Research Agreements - Schedule of Changes in Fair Value of Equity Investment (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesAdditionalInformationDetails" id="Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesAdditionalInformationDetails">
        <link:definition>100440 - Disclosure - Liability Related to the Sale of Future Royalties - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesScheduleOfActivityWithinLiabilityRelatedToSaleOfFutureRoyaltiesDetails" id="Role_DisclosureLiabilityRelatedToSaleOfFutureRoyaltiesScheduleOfActivityWithinLiabilityRelatedToSaleOfFutureRoyaltiesDetails">
        <link:definition>100450 - Disclosure - Liability Related to the Sale of Future Royalties - Schedule of Activity Within Liability Related to Sale of Future Royalties (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureStockBasedAwardsAdditionalInformationDetails" id="Role_DisclosureStockBasedAwardsAdditionalInformationDetails">
        <link:definition>100460 - Disclosure - Stock-Based Awards - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureStockBasedAwardsSummaryOfStockBasedCompensationExpenseDetails" id="Role_DisclosureStockBasedAwardsSummaryOfStockBasedCompensationExpenseDetails">
        <link:definition>100470 - Disclosure - Stock-Based Awards - Summary of Stock-Based Compensation Expense (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureNetLossPerShareOutstandingSharesOfCommonStockEquivalentsExcludedFromComputationOfDilutedNetLossPerShareDetails" id="DisclosureNetLossPerShareOutstandingSharesOfCommonStockEquivalentsExcludedFromComputationOfDilutedNetLossPerShareDetails">
        <link:definition>100480 - Disclosure - Net Loss Per Share - Outstanding Shares of Common Stock Equivalents Excluded from Computation of Diluted Net Loss per Share (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/Role_DisclosureEquityTransactionsAdditionalInformationDetails" id="Role_DisclosureEquityTransactionsAdditionalInformationDetails">
        <link:definition>100490 - Disclosure - Equity Transactions - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureAccumulatedOtherComprehensiveIncomeScheduleOfTotalAccumulatedOtherComprehensiveLossDetails" id="DisclosureAccumulatedOtherComprehensiveIncomeScheduleOfTotalAccumulatedOtherComprehensiveLossDetails">
        <link:definition>100500 - Disclosure - Accumulated Other Comprehensive Income - Schedule of Total Accumulated Other Comprehensive Loss (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.ultragenyx.com/20220630/taxonomy/role/DisclosureSubsequentEventAdditionalInformationDetails" id="DisclosureSubsequentEventAdditionalInformationDetails">
        <link:definition>100510 - Disclosure - Subsequent Event - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xsd:appinfo>
  </xsd:annotation>
  <xsd:element id="rare_CostSharingPaymentsAbstract" name="CostSharingPaymentsAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ResearchGrantAgreementAbstract" name="ResearchGrantAgreementAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_AdditionalMilestonePayments" name="AdditionalMilestonePayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_AllocatedShareBasedCompensationExpenseNetOfCapitalizedInventoryCost" name="AllocatedShareBasedCompensationExpenseNetOfCapitalizedInventoryCost" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_AvailableForSaleSecuritiesContractualMaturity" name="AvailableForSaleSecuritiesContractualMaturity" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_AvailableForSaleSecuritiesUnrealizedLossPositionAccumulatedLoss" name="AvailableForSaleSecuritiesUnrealizedLossPositionAccumulatedLoss" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_AvailableForSaleSecuritiesUnrealizedLossPositionTwelveMonthsOrLongerFairValue" name="AvailableForSaleSecuritiesUnrealizedLossPositionTwelveMonthsOrLongerFairValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_BusinessCombinationUpfrontPayment" name="BusinessCombinationUpfrontPayment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_CollaborativeArrangementsEffectiveReductionOfExpense" name="CollaborativeArrangementsEffectiveReductionOfExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_CollaborativeArrangementsEffectiveReductionOfExpenseInResearchAndDevelopmentExpenses" name="CollaborativeArrangementsEffectiveReductionOfExpenseInResearchAndDevelopmentExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_CollaborativeArrangementsEffectiveReductionOfExpenseInSellingGeneralAndAdministrativeExpenses" name="CollaborativeArrangementsEffectiveReductionOfExpenseInSellingGeneralAndAdministrativeExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_CommercialMilestonePayment" name="CommercialMilestonePayment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_CommercialMilestonePayments" name="CommercialMilestonePayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ContractLiabilitiesCurrent" name="ContractLiabilitiesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_ContractLiabilitiesNoncurrent" name="ContractLiabilitiesNoncurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_ContractWithCustomerAssetsLiabilityAdditionsDuringPeriod" name="ContractWithCustomerAssetsLiabilityAdditionsDuringPeriod" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ContractWithCustomerAssetsLiabilityCurrent" name="ContractWithCustomerAssetsLiabilityCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ContractWithCustomerAssetsLiabilityDeductionsDuringPeriod" name="ContractWithCustomerAssetsLiabilityDeductionsDuringPeriod" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_CostOfSales" name="CostOfSales" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_CostOfSalesAndOperatingExpenses" name="CostOfSalesAndOperatingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_DevelopmentAndTransitionCosts" name="DevelopmentAndTransitionCosts" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_EligibleFutureMilestonePayments" name="EligibleFutureMilestonePayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_EquityInvestmentsNoncurrent" name="EquityInvestmentsNoncurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_EstimatedReimbursementOfDeliveringLicenseAndTechnologyServices" name="EstimatedReimbursementOfDeliveringLicenseAndTechnologyServices" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_ExclusiveOptionsSubjectToOptionExercisePeriod" name="ExclusiveOptionsSubjectToOptionExercisePeriod" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_FairValueOfSaleOfShares" name="FairValueOfSaleOfShares" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_FutureContingentMilestonePayments" name="FutureContingentMilestonePayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_IncreaseDecreaseInAccountsPayableAccruedLiabilitiesAndOtherOperatingLiabilities" name="IncreaseDecreaseInAccountsPayableAccruedLiabilitiesAndOtherOperatingLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_IncreaseDecreaseInContractLiabilities" name="IncreaseDecreaseInContractLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_InterestRateOfFutureRoyaltyPayments" name="InterestRateOfFutureRoyaltyPayments" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="rare_IssuanceOfCommonStockInConnectionWithLicenseAgreementNetOfIssuanceCostsShares" name="IssuanceOfCommonStockInConnectionWithLicenseAgreementNetOfIssuanceCostsShares" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_IssuanceOfCommonStockUnderEquityPlanAwardsNetOfTax" name="IssuanceOfCommonStockUnderEquityPlanAwardsNetOfTax" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_IssuanceOfCommonStockUnderEquityPlanAwardsNetOfTaxShares" name="IssuanceOfCommonStockUnderEquityPlanAwardsNetOfTaxShares" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_IssuanceOfCommonStockUponExerciseOfWarrantsAndUnderEquityPlanAwardsNetOfTax" name="IssuanceOfCommonStockUponExerciseOfWarrantsAndUnderEquityPlanAwardsNetOfTax" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_IssuanceOfCommonStockUponExerciseOfWarrantsAndUnderEquityPlanAwardsNetOfTaxShares" name="IssuanceOfCommonStockUponExerciseOfWarrantsAndUnderEquityPlanAwardsNetOfTaxShares" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_IssuanceOfCommonStockValueInConnectionWithLicenseAgreement" name="IssuanceOfCommonStockValueInConnectionWithLicenseAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_LiabilityRelatedToSaleOfFutureRoyalties" name="LiabilityRelatedToSaleOfFutureRoyalties" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_NonCashCollaborationRoyaltyRevenue" name="NonCashCollaborationRoyaltyRevenue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_NonCashInterestExpenseOnLiabilityRelatedToSaleOfFutureRoyalties" name="NonCashInterestExpenseOnLiabilityRelatedToSaleOfFutureRoyalties" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_NonCashInterestExpenseOnLiabilityRelatedToSaleOfFutureRoyaltiesAndCapitalizedToPropertyPlantAndEquipment" name="NonCashInterestExpenseOnLiabilityRelatedToSaleOfFutureRoyaltiesAndCapitalizedToPropertyPlantAndEquipment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_NonCashInterestExpenseOnLiabilityRelatedToTheSaleOfFutureRoyaltiesCapitalizedIntoEndingPropertyPlantAndEquipment" name="NonCashInterestExpenseOnLiabilityRelatedToTheSaleOfFutureRoyaltiesCapitalizedIntoEndingPropertyPlantAndEquipment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_OperatingAndFinanceLeaseLiabilityCurrent" name="OperatingAndFinanceLeaseLiabilityCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_OperatingAndFinanceLeaseLiabilityFromObtainingRightOfUseAssets" name="OperatingAndFinanceLeaseLiabilityFromObtainingRightOfUseAssets" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_OperatingAndFinanceLeaseLiabilityNoncurrent" name="OperatingAndFinanceLeaseLiabilityNoncurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_OptionExtensionPremium" name="OptionExtensionPremium" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_OptionExtensionRightToAcquireSubjectToDescription" name="OptionExtensionRightToAcquireSubjectToDescription" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_OptionToSellCommonStockAggregateOfferingPrice" name="OptionToSellCommonStockAggregateOfferingPrice" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_PaymentFromSaleOfFutureRoyalties" name="PaymentFromSaleOfFutureRoyalties" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_PaymentRequiredToRetainPRV" name="PaymentRequiredToRetainPRV" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_PaymentsMadeUnderAgreement" name="PaymentsMadeUnderAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_PercentageOfCashValueOfConsiderationReceived" name="PercentageOfCashValueOfConsiderationReceived" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="rare_PercentageOfGrossAccountsReceivableBalance" name="PercentageOfGrossAccountsReceivableBalance" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="rare_PercentageOfGrossAccountsReceivablesFromDifferentCustomer" name="PercentageOfGrossAccountsReceivablesFromDifferentCustomer" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_PercentageOfRightToReceiveRoyaltyPaymentsOnNetSales" name="PercentageOfRightToReceiveRoyaltyPaymentsOnNetSales" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_PremiumFromStockPurchaseAgreement" name="PremiumFromStockPurchaseAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_PriorityReviewVoucher" name="PriorityReviewVoucher" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ProceedsFromIssuanceOfCommonStockAtMarketOffering" name="ProceedsFromIssuanceOfCommonStockAtMarketOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ProceedsFromIssuanceOfCommonStockInConnectionWithLicenseAgreement" name="ProceedsFromIssuanceOfCommonStockInConnectionWithLicenseAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ProceedsFromRoyaltiesReceivedFinancingActivities" name="ProceedsFromRoyaltiesReceivedFinancingActivities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ProceedsFromSaleOfFutureRoyalties" name="ProceedsFromSaleOfFutureRoyalties" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ProfitLossSharingPercentageOnCommercializingProducts" name="ProfitLossSharingPercentageOnCommercializingProducts" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ProfitLossSharingPercentageOnNetSales" name="ProfitLossSharingPercentageOnNetSales" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ReceivableRelatedToLicenseAgreementCurrent" name="ReceivableRelatedToLicenseAgreementCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_ResearchClinicalStudyAndManufacturingExpenses" name="ResearchClinicalStudyAndManufacturingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_RevenueSharePercentageOnCommercializedProductsRangeMidToHigh" name="RevenueSharePercentageOnCommercializedProductsRangeMidToHigh" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_RoyaltiesTransactionCostsNet" name="RoyaltiesTransactionCostsNet" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_RoyaltyAgreementTerminationDescription" name="RoyaltyAgreementTerminationDescription" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_RoyaltyAgreementTerminationThresholdAmount" name="RoyaltyAgreementTerminationThresholdAmount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_RoyaltyPercentageOnNetSales" name="RoyaltyPercentageOnNetSales" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesAvailableForGrantBeginningDate" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesAvailableForGrantBeginningDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesAvailableForGrantEndingDate" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesAvailableForGrantEndingDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_StockIssuedDuringPeriodSharesAtMarketOffering" name="StockIssuedDuringPeriodSharesAtMarketOffering" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_StockIssuedDuringPeriodValueAtMarketOffering" name="StockIssuedDuringPeriodValueAtMarketOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_TransactionPriceOfLicenseAgreement" name="TransactionPriceOfLicenseAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="rare_UpfrontPaymentForInProcessResearchAndDevelopmentExpense" name="UpfrontPaymentForInProcessResearchAndDevelopmentExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_UpfrontPaymentsOfCollaboration" name="UpfrontPaymentsOfCollaboration" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="rare_CostSharingPaymentsLineItems" name="CostSharingPaymentsLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_LiabilityRelatedToSaleOfFutureRoyaltiesLineItems" name="LiabilityRelatedToSaleOfFutureRoyaltiesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OrganizationAndNatureOfBusinessLineItems" name="OrganizationAndNatureOfBusinessLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_StockholdersEquityLineItems" name="StockholdersEquityLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_AbeonaMember" name="AbeonaMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ArcturusResearchCollaborationAndLicenseAgreementMember" name="ArcturusResearchCollaborationAndLicenseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CertificateOfDepositsAndTimeDepositsMember" name="CertificateOfDepositsAndTimeDepositsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CollaborationAndLicenseMember" name="CollaborationAndLicenseMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CollaborationAndRoyaltyMember" name="CollaborationAndRoyaltyMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CommercialAndDevelopmentActivityReimbursementsMember" name="CommercialAndDevelopmentActivityReimbursementsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CrysvitaMember" name="CrysvitaMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_DaiichiSankyoCoLtdMember" name="DaiichiSankyoCoLtdMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_DebtSecuritiesInGovernmentSponsoredEntitiesMember" name="DebtSecuritiesInGovernmentSponsoredEntitiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_DojolviMember" name="DojolviMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_EmploymentInducementPlanMember" name="EmploymentInducementPlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_EuropeanUnionAndSwitzerlandAndTurkeyMember" name="EuropeanUnionAndSwitzerlandAndTurkeyMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_GeneTxBiotherapeuticsLLCMember" name="GeneTxBiotherapeuticsLLCMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_GenetxMember" name="GenetxMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_HeLAPCLPlatformMember" name="HeLAPCLPlatformMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_InvestmentsInArcturusAndSolidCommonStockMember" name="InvestmentsInArcturusAndSolidCommonStockMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_KyowaKirinCollaborationMember" name="KyowaKirinCollaborationMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_LicenseAndCollaborationAgreementMember" name="LicenseAndCollaborationAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_LicenseAndTechnologyAccessAgreementMember" name="LicenseAndTechnologyAccessAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_LicensesAgreementMember" name="LicensesAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_MepseviiMember" name="MepseviiMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_MereoBioPharma3LimitedMember" name="MereoBioPharma3LimitedMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OmersMember" name="OmersMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OpenMarketSaleMember" name="OpenMarketSaleMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OptionsToPurchaseCommonStockRestrictedStockUnitsAndPerformanceStockUnitsMember" name="OptionsToPurchaseCommonStockRestrictedStockUnitsAndPerformanceStockUnitsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OtherMember" name="OtherMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_PclAndHek293PlatformsMember" name="PclAndHek293PlatformsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ProfitShareRevenueAndRoyaltiesMember" name="ProfitShareRevenueAndRoyaltiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ProgramAgreementAndUnitholderOptionAgreementMember" name="ProgramAgreementAndUnitholderOptionAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_RegeneronPharmaceuticalsIncMember" name="RegeneronPharmaceuticalsIncMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ResearchDevelopmentAndCommercializeAAVGeneTherapyProductsAgreementMember" name="ResearchDevelopmentAndCommercializeAAVGeneTherapyProductsAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_RoyaltyPurchaseAgreementMember" name="RoyaltyPurchaseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_RPIFinanceTrustMember" name="RPIFinanceTrustMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_SolidAndArcturusMember" name="SolidAndArcturusMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_SolidBiosciencesIncMember" name="SolidBiosciencesIncMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_StockPurchaseAgreementMember" name="StockPurchaseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_SublicenseAgreementMember" name="SublicenseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_TimeDepositsMember" name="TimeDepositsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_TwoThousandFourteenEmployeeStockPurchasePlanMember" name="TwoThousandFourteenEmployeeStockPurchasePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_TwoThousandFourteenIncentivePlanMember" name="TwoThousandFourteenIncentivePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_UnitedStatesAndCanadaMember" name="UnitedStatesAndCanadaMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_USAndCanadaMember" name="USAndCanadaMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_USGovernmentTreasuryAndAgencySecuritiesMember" name="USGovernmentTreasuryAndAgencySecuritiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_CostSharingPaymentsTable" name="CostSharingPaymentsTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_LiabilityRelatedToSaleOfFutureRoyaltiesTable" name="LiabilityRelatedToSaleOfFutureRoyaltiesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_OrganizationAndNatureOfBusinessTable" name="OrganizationAndNatureOfBusinessTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_StockholdersEquityTable" name="StockholdersEquityTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="rare_ScheduleOfActivityWithinLiabilityRelatedToSaleOfFutureRoyaltiesTableTextBlock" name="ScheduleOfActivityWithinLiabilityRelatedToSaleOfFutureRoyaltiesTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ScheduleOfChangesInFairValueOfEquityInvestmentTableTextBlock" name="ScheduleOfChangesInFairValueOfEquityInvestmentTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ScheduleOfChangesInFairValueOfInvestmentInSecuritiesTableTextBlock" name="ScheduleOfChangesInFairValueOfInvestmentInSecuritiesTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ScheduleOfCollaborationAndRoyaltyRevenueTableTextBlock" name="ScheduleOfCollaborationAndRoyaltyRevenueTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_ScheduleOfCostSharingPaymentsTableTextBlock" name="ScheduleOfCostSharingPaymentsTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_CollaborativeArrangementAndNoncollaborativeArrangementTransactionsDisclosureTextBlock" name="CollaborativeArrangementAndNoncollaborativeArrangementTransactionsDisclosureTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="rare_LiabilityRelatedToSaleOfFutureRoyaltiesTextBlock" name="LiabilityRelatedToSaleOfFutureRoyaltiesTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
</xsd:schema>
