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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2015-07-06</periodOfReport>

    <noSecuritiesOwned>1</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001338042</issuerCik>
        <issuerName>Aegerion Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>AEGR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001236371</rptOwnerCik>
            <rptOwnerName>PERRY GREGORY D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O AEGERION PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MAIN STREET, SUITE 800</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Financial Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jennifer Fitzpatrick, as attorney-in-fact</signatureName>
        <signatureDate>2015-07-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
