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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-03-03</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001557533</rptOwnerCik>
            <rptOwnerName>Ajer Jeffrey Robert</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BIOMARIN PHARMACEUTICAL INC.,</rptOwnerStreet1>
            <rptOwnerStreet2>105 DIGITAL DRIVE</rptOwnerStreet2>
            <rptOwnerCity>NOVATO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94949</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>EVP, Chief Commercial Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2020-03-03</value>
                <footnoteId id="F1"/>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>9586</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>71530</value>
                    <footnoteId id="F4"/>
                </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 2017 Equity Incentive Plan based on the level of the Issuer's total adjusted net product revenues for the fiscal year ended December 31, 2019 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 15, 2020, 2021 and 2022, 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">On June 7, 2019, the reporting person filed a Form 4 which inadvertently over reported the total amount of securities beneficially owned by the reporting person by 50 shares.  This Form 4 corrects such error by decreasing the total amount of securities beneficially owned by the reporting person by such 50 shares.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Eric Fleekop, Attorney-in-Fact</signatureName>
        <signatureDate>2020-03-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
