<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-05-08</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001478242</issuerCik>
        <issuerName>Quintiles Transnational Holdings Inc.</issuerName>
        <issuerTradingSymbol>Q</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001495741</rptOwnerCik>
            <rptOwnerName>TPG Group Holdings (SBS) Advisors, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TPG GLOBAL, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>301 COMMERCE STREET, SUITE 3300</rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001107479</rptOwnerCik>
            <rptOwnerName>TPG Advisors III, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TPG GLOBAL, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>301 COMMERCE STREET, SUITE 3300</rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000860866</rptOwnerCik>
            <rptOwnerName>BONDERMAN DAVID</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TPG GLOBAL, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>301 COMMERCE STREET, SUITE 3300</rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001099776</rptOwnerCik>
            <rptOwnerName>COULTER JAMES G</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TPG GLOBAL, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>301 COMMERCE STREET, SUITE 3300</rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Shares</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>26481658</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Explanation of Responses</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">David Bonderman and James G. Coulter are officers and sole shareholders of each of TPG Advisors III, Inc. (&quot;Advisors III&quot;) and TPG Group Holdings (SBS) Advisors, Inc. (&quot;Group Advisors&quot; and, together with Advisors III and Messrs. Bonderman and Coulter, the &quot;Reporting Persons&quot;).</footnote>
        <footnote id="F2">Advisors III is the general partner of TPG GenPar III, L.P., which is the general partner of TPG Partners III, L.P., which is the managing member of TPG Quintiles Holdco LLC (&quot;Holdco I&quot;), which directly holds 8,264,038 shares of Common Stock (&quot;Shares&quot;) of Quintiles Transnational Holdings Inc. (the &quot;Issuer&quot;).</footnote>
        <footnote id="F3">Group Advisors is the general partner of TPG Group Holdings (SBS), L.P., which is the sole member of TPG Holdings I-A, LLC, which is the general partner of TPG Holdings I, L.P., which is the sole member of each of (i) TPG GenPar V Advisors, LLC, which is the general partner of TPG GenPar V, L.P., which is the general partner of TPG Partners V, L.P., which is the managing member of each of TPG Quintiles Holdco II LLC (&quot;Holdco II&quot;), which directly holds 17,301,294 Shares, and TPG Quintiles Holdco IV LLC (&quot;Holdco IV&quot;), which directly holds 100,000 Shares, and (ii) TPG Biotechnology GenPar II Advisors, LLC, which is the general partner of TPG Biotechnology GenPar II, L.P., which is the general partner of TPG Biotechnology Partners II, L.P., which is the sole member of TPG Quintiles Holdco III LLC (&quot;Holdco III&quot; and, together with Holdco I, Holdco II and Holdco IV, the &quot;TPG Funds&quot;), which directly holds 816,326 Shares.</footnote>
        <footnote id="F4">Because of the relationship between the Reporting Persons and the TPG Funds, the Reporting Persons may be deemed to beneficially own the securities reported herein to the extent of the greater of their respective direct or indirect pecuniary interests in the profits or capital accounts of the TPG Funds.  Each Reporting Person and each TPG Fund disclaims beneficial ownership of the securities reported herein, except to the extent of such Reporting Person's or TPG Fund's pecuniary interest therein, if any.</footnote>
        <footnote id="F5">The TPG Funds have entered into a Shareholders Agreement, dated as of January 22, 2008 (as supplemented and amended, the &quot;Shareholders Agreement&quot;), with certain other holders (the &quot;Holders&quot;) of Shares.  Because of the relationship between the TPG Funds and the Holders as a result of the Shareholders Agreement, the Reporting Persons may be deemed, pursuant to Rule 13d-3 under the Securities Exchange Act of 1934, as amended (the &quot;Exchange Act&quot;), to beneficially own the 70,460,403 Shares held in the aggregate by the Holders.  Each Reporting Person and each TPG Fund disclaims beneficial ownership of the Shares held by the Holders.</footnote>
        <footnote id="F6">Pursuant to Rule 16a-1(a)(4) under the Exchange Act, this filing shall not be deemed an admission that the Reporting Persons are, for purposes of Section 16 of the Exchange Act or otherwise, the beneficial owners of any equity securities in excess of their respective pecuniary interests.</footnote>
    </footnotes>

    <remarks>(7) The Reporting Persons are jointly filing this Form 3 pursuant to Rule 16a-3(j) under the Exchange Act.

(8) Ronald Cami is signing on behalf of both Messrs. Bonderman and Coulter pursuant to the authorization and designation letters dated July 1, 2010, which were previously filed with the Securities and Exchange Commission.</remarks>

    <ownerSignature>
        <signatureName>/s/ Ronald Cami, Vice President, TPG Group Holdings (SBS) Advisors, Inc. (7)</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Ronald Cami, Vice President, TPG Advisors III, Inc. (7)</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Ronald Cami on behalf of David Bonderman (7)(8)</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Ronald Cami on behalf of James G. Coulter (7)(8)</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
