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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-05-11</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000919722</issuerCik>
        <issuerName>SUPERGEN INC</issuerName>
        <issuerTradingSymbol>SUPG</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001236365</rptOwnerCik>
            <rptOwnerName>MANUSO JAMES S J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SUPERGEN, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>4140 DUBLIN BOULEVARD, SUITE 200</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94568</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>President/CEO</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>11.27</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-05-11</value>
                <footnoteId id="F1"/>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>250000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-05-11</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-01-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>250000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>250000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On January 2, 2004, reporting person was granted an option to buy 1,000,000 shares of Common Stock under the Issuer's 2003 Stock Plan.  250,000 of the shares subject to such option grant were to vest upon satisfaction of certain performance milestones.  On May 11, 2006 these performance milestones were deemed to have been met and the 250,00 option shares became vested.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ James S.J. Manuso</signatureName>
        <signatureDate>2006-05-15</signatureDate>
    </ownerSignature>
</ownershipDocument>
