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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-12-27</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000874015</issuerCik>
        <issuerName>IONIS PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>IONS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001838539</rptOwnerCik>
            <rptOwnerName>Schneider Eugene</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O IONIS PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>2855 GAZELLE COURT</rptOwnerStreet2>
            <rptOwnerCity>CARLSBAD,</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92010</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>EVP, Chf Clinical Develop Offc</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2118</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>61.57</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2022-01-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6100.0</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>63.18</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2022-03-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>18750</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>61.68</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2023-01-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11000.0</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>47.34</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2024-01-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>25000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>49.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2025-01-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>25000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>45.04</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2025-07-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>53.77</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-01-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>19658</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>60.89</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F8"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-01-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>26000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F14"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F9"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F9"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1041.0</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F14"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F10"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F10"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2777</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F14"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F11"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F11"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>833.0</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F14"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F12"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F12"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6552</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F14"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F13"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F13"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11556</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Grant on 01/02/2015 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 1/02/2016.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 6,100 shares on 12/27/2020</footnote>
        <footnote id="F2">Grant on 04/01/2015 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 04/01/2016.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 18,750 shares on 12/27/2020</footnote>
        <footnote id="F3">Grant on 01/04/2016 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 1/4/2017.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 11,000 shares on 12/27/2020</footnote>
        <footnote id="F4">Grant on 01/03/2017 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 1/03/2018.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 24,479 shares on 12/27/2020</footnote>
        <footnote id="F5">Grant on 01/02/2018 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 1/02/2019.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 18,229 shares on 12/27/2020</footnote>
        <footnote id="F6">Grant on 07/29/2018 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 07/29/2019.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 4,375 shares on 12/27/2020</footnote>
        <footnote id="F7">Grant on 01/02/2019 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option vested and became exercisable on 01/02/2020.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 9,420 shares on 12/27/2020</footnote>
        <footnote id="F8">Grant on 01/02/2020 to reporting person of stock options under the Ionis Pharmaceuticals, Inc. Amended and Restated 2011 Equity Incentive Plan.  25% of the shares subject to the option will be vested and become exercisable on 01/02/2021.  Thereafter, the remaining shares subject to the option vested and became exercisable in 36 equal monthly installments. The option is exercisable as to 0 shares on 12/27/2020</footnote>
        <footnote id="F9">The restricted stock units vest in four equal annual installments, the first installment vesting was on January 15, 2018.  Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.  The RSU shall be fully vested on January 15, 2021.</footnote>
        <footnote id="F10">The restricted stock units vest in four equal annual installments, the first installment vesting was on January 15, 2019.  Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.  The RSU shall be fully vested on January 15, 2022.</footnote>
        <footnote id="F11">The restricted stock units vest in four equal annual installments, the first installment vesting was on October 15, 2019.  Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.  The RSU shall be fully vested on October 15, 2022.</footnote>
        <footnote id="F12">The restricted stock units vest in four equal annual installments, the first installment vesting was on January 15,2020.  Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.  The RSU shall be fully vested on January 15, 2023.</footnote>
        <footnote id="F13">The restricted stock units vest in four equal annual installments, the first installment vesting on January 15, 2021.  Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.  The RSU shall be fully vested on January 15, 2024.</footnote>
        <footnote id="F14">Each restricted stock unit represents a contingent right to receive one share of Ionis common stock or its equivalent cash value</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/Patrick R. O'Neil, attorney-in-fact</signatureName>
        <signatureDate>2021-01-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
