<PAGE>
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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
 
                             WASHINGTON, D.C. 20549
 
                            ------------------------
 
                                  FORM 10-K/A
 
            /X/ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE
                      SECURITIES AND EXCHANGE ACT OF 1934
 
                  FOR THE FISCAL YEAR ENDED DECEMBER 31, 1996
 
          / / TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE
                        SECURITIES EXCHANGE ACT OF 1934
 
          FOR THE TRANSITION PERIOD FROM              TO
                         COMMISSION FILE NUMBER 0-21643
 
                            ------------------------
 
                             CV THERAPEUTICS, INC.
 
             (Exact name of Registrant as specified in its charter)
 
<TABLE>
<S>                            <C>
          DELAWARE                         43-1570294
(State or other jurisdiction   (IRS Employer Identification No.)
             of
      incorporation or
        organization)
</TABLE>
 
                 3172 PORTER DRIVE, PALO ALTO, CALIFORNIA 94304
          (Address of principal executive offices, including zip code)
 
                                 (415) 812-0585
              (Registrant's telephone number, including area code)
 
        Securities registered pursuant to Section 12(b) of the Act: NONE
 
Securities registered pursuant to Section 12(g) of the Act: COMMON STOCK, $.001
                                   PAR VALUE
 
    Indicate by check mark whether the Registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities and Exchange Act
of 1934 during the preceding 12 months (or for such shorter period that the
Registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes /X/   No
 
    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained to be
the best Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. /X/
 
    The approximate aggregate market value of the Common Stock held by
nonaffiliates of the Registrant, based upon the last sale price of the Common
Stock reported on the Nasdaq Stock Market was $38,466,767 as of February 28,
1997.
 
     The number of shares of Common Stock outstanding as of March 10, 1997 was
                                   6,858,635.
 
                      DOCUMENTS INCORPORATED BY REFERENCE
 
    Certain exhibits filed with the Registrant's Registration Statement on Form
S-1 (Registration No. 333-12675), as amended, and certain exhibits filed with
the Registrant's Registration Statement on Form S-8 (Registration No. 333-19389)
are incorporated herein by reference into Part IV of this report.
 
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<PAGE>
    Item 11 of CV Therapeutics, Inc.'s Annual Report on Form 10-K for the year
ended December 31, 1996 is hereby amended to read as follows:
 
ITEM 11. EXECUTIVE COMPENSATION
 
DIRECTOR COMPENSATION
 
    Other than Isaac Stein and Barbara McNeil, who receive $1,000 per meeting
attended as described below, the Company's directors currently do not receive
cash compensation for service on the Board of Directors or any committee
thereof, but directors may be reimbursed for reasonable expenses in connection
with attendance at Board and committee meetings.
 
    In July 1994, the Board of Directors adopted and in July 1995, the
stockholders approved the Non-Employee Directors' Stock Option Plan (the
"Directors' Plan"). On September 23, 1996, the Board of Directors amended and
restated, and on October 29, 1996, the stockholders approved the amended and
restated Directors' Plan. The Directors' Plan provides for automatic grants of
options to purchase shares of Common Stock to non-employee directors of the
Company ("Non-Employee Directors"). Pursuant to the terms of the Directors'
Plan, each Non-Employee Director is automatically granted an option to purchase
shares of Common Stock. On September 8, 1996, each Non-Employee Director was
granted an option to purchase 500 shares. These options vest at the rate of
1/36 per month. Upon the amendment and restatement of the Directors' Plan, each
Non-Employee Director was granted an additional option to purchase 15,000
shares. Each subsequently elected Non-Employee Director will also be granted an
option to purchase 15,000 shares at his or her election. These options for
15,000 shares vest as to 33.33% of the shares 12 months from the date of grant,
and at the rate of 1/36 per month thereafter, if the Non-Employee Director
provides services to the Company or its affiliates through the applicable
vesting date. In addition, at each annual meeting of the Company's stockholders
starting in 1997, each Non-Employee Director will be granted an option to
purchase 5,000 shares, which will vest 12 months from the date of grant if the
Non-Employee Director provides services to the Company or its affiliates through
such date.
 
    The exercise price of options granted under the Directors' Plan must equal
the fair market value of the Common Stock on the date of grant; provided,
however, that prior to the September 1996 amendment and restatement of the
Directors' Plan, the exercise price of options granted to any person possessing
more than 10% of the total combined voting power of all classes of stock of the
Company or of any of its affiliates was 110% of the fair market value on the
date of grant. No option granted under the Directors' Plan may be exercised
after the expiration of ten years from date it was granted. No option may be
transferred by the optionee other than by will or the laws of descent or
distribution, provided that an optionee may designate a beneficiary who may
exercise the option following the optionee's death. Upon certain changes in
control of the Company, outstanding options will be assumed or substituted by
the surviving corporation. The Directors' Plan will terminate in September 2006,
unless earlier terminated by the Board.
 
    Under the terms of a Separation and Consulting Agreement between the Company
and Thomas L. Gutshall, the Company accepted Mr. Gutshall's resignation as
President and Chief Operating Officer effective September 2, 1996 and Mr.
Gutshall agreed to continue to serve as a member of the Company's Board of
Directors and to serve as a consultant to the Company through December 31, 1998.
Pursuant to this agreement, Mr. Gutshall received $22,750 as compensation for
his consulting services in the fiscal year ended December 31, 1996. Mr. Gutshall
will receive $3,500 per month as consulting fees during the fiscal years ending
December 31, 1997 and 1998.
 
    Under the terms of a Consulting Agreement for Individual Consultants between
the Company and Barbara J. McNeil, M.D., Ph.D., the Company agreed to pay a
fixed fee of $1,000 per day as compensation for Dr. McNeil's services. In the
fiscal year ended December 31, 1996, Dr. McNeil earned $2,000 as compensation
for her services. The Company paid that amount to Dr. McNeil in 1997. The
Company may terminate this agreement for any reason upon written notice.
 
                                       1
<PAGE>
    Under the terms of a Consulting Agreement for Individual Consultants between
the Company and Isaac Stein, Mr. Stein received $6,000 as compensation for his
services in the fiscal year ended December 31, 1996. In addition, in September
1996 the Company granted Mr. Stein an option to purchase 10,000 shares of Common
Stock outside the Directors' Plan at an exercise price of $2.50 per share. The
option vests over a three year period. The Company may terminate the agreement
for any reason upon written notice.
 
    As compensation for consulting services rendered in the fiscal year ended
December 31, 1996, the Company paid Dr. Sevastopoulos $30,000 in 1997. In
addition, in September 1996, the Company granted him an option to purchase 5,000
shares of Common Stock at an exercise price of $2.50 per share. The option grant
vests over a three year period.
 
                                       2
<PAGE>
COMPENSATION OF EXECUTIVE OFFICERS
 
    The following table sets forth for the fiscal years ended December 31, 1995
and 1996 certain compensation awarded or paid to, or earned by the Company's
Chief Executive Officer and the Company's next four most highly compensated
officers during the fiscal year ended December 31, 1996 (collectively, the
"Named Executive Officers"):
 
                           SUMMARY COMPENSATION TABLE
 
<TABLE>
<CAPTION>
                                                                                                  LONG-TERM
                                                                                                COMPENSATION
                                                                ANNUAL COMPENSATION             -------------
                                                     -----------------------------------------   SECURITIES
                                                                               OTHER ANNUAL      UNDERLYING        ALL OTHER
NAME AND PRINCIPAL POSITION                 YEAR     SALARY($)   BONUS($)     COMPENSATION($)    OPTIONS(#)     COMPENSATION($)
----------------------------------------  ---------  ---------  -----------  -----------------  -------------  -----------------
<S>                                       <C>        <C>        <C>          <C>                <C>            <C>
Louis G. Lange, M.D., Ph.D.                 1995       250,000      --              30,000(1)        55,000           --
  Chairman of the Board                     1996       250,000      35,000(2)        94,242(3)       65,000           --
  and Chief Executive Officer
Kathleen A. Stafford                        1995         5,000      --              --               35,250           95,425(4)
  Chief Financial Officer                   1996       109,800      12,500(5)        --              14,250           --
Michael M. Wick, M.D., Ph.D.                1995       160,045      30,000          --               62,500           --
  Senior Vice President,                    1996       190,000      15,000(6)        --              27,500           --
  Research
Andrew W. Wolff, M.D.                       1995       175,500      17,500          --                7,500           --
  Vice President, Clinical                  1996       184,000      20,000(7)        --              22,500           --
  Research and Development
George F. Schreiner, M.D., Ph.D.            1995       159,750      --              26,625(1)        12,800           --
  Vice President, Clinical                  1996       163,000       5,000(9)        22,785(10)      15,000           --
  Research and Development (8)
</TABLE>
 
------------------------
 
(1) Consists of amounts forgiven on loan obligations.
 
(2) Consists of $10,000 paid in 1996 based upon Dr. Lange's performance in 1995
    and $25,000 representing the dollar value of shares awarded in 1997 based
    upon Dr. Lange's performance in 1996. The dollar value was calculated by
    multiplying the market value on the day prior to the date of grant ($8.50)
    by the number of shares awarded.
 
(3) Consists of $92,880 forgiven on loan obligations and $1,362 paid to satisfy
    related tax obligations. See "Certain Transactions."
 
(4) Consists of fees paid for consulting services. Ms. Stafford served as a
    consultant to the Company from May 1995 through November 1995 before
    becoming the Chief Financial Officer on December 1, 1995.
 
(5) Consists of the dollar value of shares awarded in 1997 based upon Ms.
    Stafford's performance in 1996. See footnote (2) for calculation of stock
    award.
 
(6) Consists of $10,000 paid in 1996 based upon Dr. Wick's performance in 1995
    and $5,000 representing the dollar value of shares awarded in 1997 based
    upon Dr. Wick's performance in 1996. See footnote (2) for calculation of
    stock award.
 
(7) Consists of $10,000 paid in 1996 based upon Dr. Wolff's performance in 1995
    and $10,000 representing the dollar value of shares awarded in 1997 based
    upon Dr. Wolff's performance in 1996. See footnote (2) for calculation of
    stock award.
 
(8) Dr. Schreiner terminated his employment with the Company in January 1997.
 
(9) Consists of a cash bonus paid in 1996 based upon Dr. Schreiner's performance
    in 1995.
 
(10) Consists of $15,066 forgiven on loan obligations, $219 paid to satisfy
    related tax obligations and $7,500 in mortgage assistance. See "Certain
    Transactions."
 
                                       3
<PAGE>
                       OPTION GRANTS IN LAST FISCAL YEAR
 
    The following table sets forth each grant of stock options made during the
fiscal year ended December 31, 1996 to each of the Named Executive Officers:
 
<TABLE>
<CAPTION>
                                                               INDIVIDUAL GRANTS
                                             ------------------------------------------------------  POTENTIAL REALIZABLE
                                                           PERCENTAGE OF                               VALUE AT ASSUMED
                                              NUMBER OF    TOTAL OPTIONS                             ANNUAL RATES OF STOCK
                                             SECURITIES     GRANTED TO                                PRICE APPRECIATION
                                             UNDERLYING    EMPLOYEES IN     EXERCISE                  FOR OPTION TERM(3)
                                               OPTIONS        FISCAL          PRICE     EXPIRATION   ---------------------
NAME                                         GRANTED(#)     YEAR(%)(1)     ($/SH) (2)      DATE        5%($)      10%($)
-------------------------------------------  -----------  ---------------  -----------  -----------  ---------  ----------
<S>                                          <C>          <C>              <C>          <C>          <C>        <C>
Louis G. Lange, M.D., Ph.D.................      65,000(4)        18.21          2.50     09/09/06     684,525   1,186,246
Kathleen A. Stafford.......................      12,000(5)         3.36          2.50     09/09/06     126,374     218,999
                                                  2,250(6)         0.63          2.50     03/27/06      23,695      41,062
Michael M. Wick, M.D., Ph.D................      27,500(5)         7.72          2.50     09/09/06     289,607     501,873
Andrew A. Wolff, M.D.......................      22,500(5)         6.32          2.50     09/09/06     236,951     410,624
George F. Schreiner, M.D., Ph.D. (7).......      15,000           4.21           2.50     04/07/97           0           0
</TABLE>
 
------------------------------
 
(1) Based on an aggregate of options to purchase 356,290 shares of the Company's
    Common Stock granted to employees and directors of, and consultants to, the
    Company during the fiscal year ended December 31, 1996, including the Named
    Executive Officers.
 
(2) The exercise price per share of each option was equal to the fair market
    value of the Common Stock on the date of grant as determined by the Board of
    Directors.
 
(3) The potential realizable value is calculated based on the term of the option
    at its time of grant (ten years). It is calculated assuming that the stock
    price on the date of grant appreciates from the date of grant at the
    indicated annual rate compounded annually for the entire term of the option
    and the option is exercised and sold on the last day of its term for the
    appreciated stock price. No gain to the optionee is possible unless the
    stock price increases over the option term.
 
(4) Twenty percent of the option vests one year from the vesting commencement
    date, with subsequent vesting at a rate of 1.67% each month until fully
    vested. The option expires ten years from the date of grant or earlier upon
    termination of employment.
 
(5) Twenty-four percent of the option vests one year from the vesting
    commencement date, with subsequent vesting at a rate of two percent per
    month until fully vested. The option expires ten years from the date of
    grant or earlier upon termination of employment.
 
(6) The option is fully vested and expires ten years from the date grant or
    earlier upon termination of employment.
 
(7) In connection with the termination of Dr. Schreiner's employment, the option
    to purchase 15,000 shares did not vest and will be cancelled on April 7,
    1997.
 
                                       4
<PAGE>
 AGGREGATE OPTION EXERCISES IN FISCAL 1996 AND DECEMBER 31, 1996 OPTION VALUES
 
    The following table sets forth the number and value of securities underlying
unexercised options held by each of the Named Executive Officers at December 31,
1996. No options were exercised by the Named Executive Officers in the fiscal
year ended December 31, 1996.
 
<TABLE>
<CAPTION>
                                                                                            VALUE OF UNEXERCISED
                                                                                           IN- THE-MONEY OPTIONS
                                                                NUMBER OF SECURITIES          AT DECEMBER 31,
                                                           UNDERLYING UNEXERCISED OPTIONS         1996($)
                                                              AT DECEMBER 31, 1996(#)           EXERCISABLE/
NAME                                                        EXERCISABLE/UNEXERCISABLE(1)      UNEXERCISABLE(2)
---------------------------------------------------------  ------------------------------  ----------------------
<S>                                                        <C>                             <C>
Louis G. Lange, M.D., Ph.D...............................              195,000/0                   890,350/0
Kathleen A. Stafford.....................................               39,500/0                   165,505/0
Michael M. Wick, M.D., Ph.D..............................               60,000/0                   251,400/0
Andrew A. Wolff, M.D.....................................               52,500/0                   219,975/0
George F. Schreiner, M.D., Ph.D..........................               68,025/0                   337,237/0
</TABLE>
 
------------------------------
 
(1) As of December 31, 1996, of the 195,000, 39,500, 60,000, 52,500 and 68,025
    option shares held by Louis G. Lange, M.D., Ph.D., Kathleen A. Stafford,
    Michael M. Wick, M.D., Ph.D., Andrew A. Wolff, M.D. and George F. Schreiner,
    M.D., Ph.D., 125,750, 27,200, 47,650, 40,175 and 33,383 option shares,
    respectively, were unvested and subject to repurchase by the Company, if
    exercised.
 
(2) Based on the fair market value of the Company's Common Stock at December 31,
    1996 ($6.69) minus the exercise price of the options.
 
                                       5
<PAGE>
                                   SIGNATURES
 
    Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Registrant has duly caused this report on Form 10-K/A
to be signed on its behalf, by the undersigned, thereunto duly authorized, in
the City of Palo Alto, County of Santa Clara, State of California, on April 25,
1997.
 
                                CV THERAPEUTICS, INC.
 
                                By:       /s/ LOUIS G. LANGE, M.D., PH.D.
                                     -----------------------------------------
                                            Louis G. Lange, M.D., Ph.D.
                                              CHAIRMAN OF THE BOARD OF
                                              CHIEF EXECUTIVE OFFICER
 
    PURSUANT TO THE REQUIREMENTS OF THE SECURITIES EXCHANGE ACT OF 1934, THIS
HAS BEEN SIGNED BY THE FOLLOWING PERSONS ON BEHALF OF THE REGISTRANT AND IN THE
CAPACITIES AND ON THE DATES INDICATED.
 
<TABLE>
<CAPTION>
          SIGNATURE                       TITLE                    DATE
------------------------------  --------------------------  -------------------
<C>                             <S>                         <C>
 
  /s/ LOUIS G. LANGE, M.D.,     Chairman of the Board &
            PH.D.                 Chief Executive Officer
------------------------------    (Principal Executive        April 25, 1997
 Louis G. Lange, M.D., Ph.D.      Officer)
 
   /s/ KATHLEEN A. STAFFORD     Chief Financial Officer
------------------------------    (Principal Financial and    April 25, 1997
     Kathleen A. Stafford         Accounting Officer)
 
    /s/ SAMUEL D. COLELLA*
------------------------------  Director                      April 25, 1997
      Samuel D. Colella
 
   /s/ THOMAS L. GUTSHALL*
------------------------------  Director                      April 25, 1997
      Thomas L. Gutshall
 
 /s/ BARBARA J. MCNEIL, M.D.,
            PH.D.*
------------------------------  Director                      April 25, 1997
Barbara J. McNeil, M.D., Ph.D.
 
 /s/ COSTA G. SEVASTOPOULOS,
            PH.D.*
------------------------------  Director                      April 25, 1997
Costa G. Sevastopoulos, Ph.D.
 
 /s/ J. LEIGHTON READ, M.D.*
------------------------------  Director                      April 25, 1997
    J. Leighton Read, M.D.
</TABLE>
 
                                       6
<PAGE>
<TABLE>
<CAPTION>
          SIGNATURE                       TITLE                    DATE
------------------------------  --------------------------  -------------------
<C>                             <S>                         <C>
       /s/ ISAAC STEIN*
------------------------------  Director                      April 25, 1997
         Isaac Stein
</TABLE>
 
*By:  /s/ LOUIS G. LANGE, M.D.,
                PH.D.
      -------------------------
        Louis G. Lange, M.D.,
                Ph.D.
 
*By:       /s/ KATHLEEN A.
              STAFFORD
      -------------------------
        Kathleen A. Stafford
 
                                       7