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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2018-02-26</periodOfReport>

    <dateOfOriginalSubmission>2018-02-28</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001048477</issuerCik>
        <issuerName>BIOMARIN PHARMACEUTICAL INC</issuerName>
        <issuerTradingSymbol>BMRN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001380710</rptOwnerCik>
            <rptOwnerName>Davis George Eric</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BIOMARIN PHARMACEUTICAL INC.</rptOwnerStreet1>
            <rptOwnerStreet2>770 LINDARO ST.</rptOwnerStreet2>
            <rptOwnerCity>SAN RAFAEL</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94901</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>EVP, General Counsel</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2018-02-26</value>
                <footnoteId id="F1"/>
            </transactionDate>
            <deemedExecutionDate>
                <value>2018-02-26</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>11601</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>94343</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Transaction Date is the date that the Issuer's Board of Directors' Compensation Committee Chair certified that the reporting person earned the Restricted Stock Units (RSUs), which are convertible into shares of the Issuer's Common Stock on a 1:1 basis.</footnote>
        <footnote id="F2">Represents the total number of RSUs earned pursuant to a calculation set forth in the performance-based RSU awards previously granted under the Issuer's 2006 Share Incentive Plan based on the level of the Issuer's total adjusted net product revenues for the fiscal year ended December 31, 2017 as set forth in the Issuer's audited financial statements.</footnote>
        <footnote id="F3">Although earned, the RSUs only vest according to the following schedule: 1/3 vests on each of March 22, 2018, 2019 and 2020, so long as the reporting person remains continuously employed with the Issuer through that date, subject to earlier vesting upon certain events.</footnote>
        <footnote id="F4">This amendment is being filed solely to correct an administrative error in the original filing regarding the number of RSUs reported as earned.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Laura Randall Woodhead, Attorney-in-Fact</signatureName>
        <signatureDate>2018-04-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
