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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-11-30</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000939767</issuerCik>
        <issuerName>EXELIXIS INC</issuerName>
        <issuerTradingSymbol>EXEL</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001202102</rptOwnerCik>
            <rptOwnerName>SCANGOS GEORGE A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O EXELIXIS INC.</rptOwnerStreet1>
            <rptOwnerStreet2>170 HARBOR WAY, PO BOX 0511</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94083-0511</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>President, CEO &amp; Director</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

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            <transactionCoding>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
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                    <value>181</value>
                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
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            </postTransactionAmounts>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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            <transactionTimeliness>
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                <transactionPricePerShare>
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    </nonDerivativeTable>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ George Scangos</signatureName>
        <signatureDate>2004-11-30</signatureDate>
    </ownerSignature>
</ownershipDocument>

