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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2019-02-11</periodOfReport>

    <dateOfOriginalSubmission>2019-02-11</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001070336</issuerCik>
        <issuerName>ACHILLION PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>ACHN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001766498</rptOwnerCik>
            <rptOwnerName>Di Donato Brian</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ACHILLION PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>1777 SENTRY PARKWAY W, BLDG 14, STE 200</rptOwnerStreet2>
            <rptOwnerCity>BLUE BELL</rptOwnerCity>
            <rptOwnerState>PA</rptOwnerState>
            <rptOwnerZipCode>19422</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>false</isDirector>
            <isOfficer>true</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
            <officerTitle>SVP, Chief Financial Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2028-08-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>200000.00</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This option was granted on August 7, 2018 and vests as to 25% of the original number of shares on the first anniversary of the grant date and as to an additional 6.25% of the original number of shares at the end of each successive three-month period thereafter.</footnote>
    </footnotes>

    <remarks>This Form 3/A amends and restates the Form 3 filed by the reporting person on February 11, 2019.</remarks>

    <ownerSignature>
        <signatureName>/s/ Brian Di Donato</signatureName>
        <signatureDate>2019-11-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
