<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>3</documentType><periodOfReport>2003-08-07</periodOfReport>
    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001031107</issuerCik>
        <issuerName>PEREGRINE SYSTEMS INC</issuerName>
        <issuerTradingSymbol>PRGND</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001258161</rptOwnerCik>
            <rptOwnerName>JENKINS JAMES</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>200 PARK AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3300</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10166</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeHolding><securityTitle><value>No securities beneficially owned</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value><footnoteId id="F1"/></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><footnotes><footnote id="F1">The reporting person does not beneficially own, directly or indirectly, any of the securities of the issuer.</footnote></footnotes><remarks/><ownerSignature><signatureName>JAMES JENKINS</signatureName><signatureDate>2003-08-18</signatureDate></ownerSignature></ownershipDocument>

