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

    <schemaVersion>X0304</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2012-01-13</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001011290</issuerCik>
        <issuerName>99 CENTS ONLY STORES</issuerName>
        <issuerTradingSymbol>NYSE: NDN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001096973</rptOwnerCik>
            <rptOwnerName>GOLD SHERRY</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O 99? ONLY STORES</rptOwnerStreet1>
            <rptOwnerStreet2>4000 UNION PACIFIC AVENUE</rptOwnerStreet2>
            <rptOwnerCity>CITY OF COMMERCE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>90023</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>6865973</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>22</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F4"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1818181</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7381224</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>7381224</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>22</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Disposed of in connection with the Agreement and Plan of Merger, dated as of October 11, 2011, by and among 99 Cents Only Stores (the &quot;Company&quot;), Number Holdings, Inc., a Delaware corporation (&quot;Parent&quot;), and Number Merger Sub, Inc., a California corporation and a wholly owned subsidiary of Parent (&quot;Merger Sub&quot;).</footnote>
        <footnote id="F2">As a result of the merger of Merger Sub with and into the Company (the &quot;Merger&quot;), each share of the Company's common stock, no par value (the &quot;Company common stock&quot;), was converted into the right to receive $22.00 in cash, without interest and less any applicable withholding taxes.</footnote>
        <footnote id="F3">Beneficially owned through Au Zone Investments #2, L.P., a limited partnership in which the reporting person has a limited partnership interest and an interest in the partnership's general partner.</footnote>
        <footnote id="F4">In connection with the Merger, the reporting person contributed 1,818,181 shares of Company common stock, valued at $22.00 per share, to Parent prior to the consummation of the Merger in accordance with the terms of that certain equity rollover letter, dated October 11, 2011, by and among Parent, the reporting person and certain other rollover investors. In exchange for the 1,818,181 shares of Company common stock, the reporting person received shares of capital stock representing approximately 6.3% of the aggregate common stock of Parent as of the closing.</footnote>
        <footnote id="F5">Beneficially owned through The Gold Revocable Trust dated October 26, 2005, a revocable trust in which the reporting person and her spouse are co-trustees.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Sherry Gold</signatureName>
        <signatureDate>2012-01-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
