<PAGE>
 
                                                                    EXHIBIT 11.1



                    PURE ATRIA CORPORATION AND SUBSIDIARIES

       COMPUTATION OF NET LOSS AND PRO FORMA NET INCOME (LOSS) PER SHARE
                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)

<TABLE>
<CAPTION>
 
                                                     YEAR  ENDED
                                                     -----------
                                                     DECEMBER 31,
                                                     ------------
                                             1996       1995       1994
                                           -------    -------    -------
<S>                                        <C>        <C>        <C>
 
Net Loss                                   $(6,657)
                                           =======
 
Pro forma net income (loss) (2)                       $(4,246)    $ 5,132
                                                      =======     =======    
                                           
Weighted average number of common          
   shares outstanding...................    39,921     33,706      24,077
                                           
Weighted average number of  preferred      
   shares outstanding on an as if          
   converted basis......................        --      3,829       9,289
                                           
Number of common stock equivalents         
   as a result of stock options            
   outstanding using the treasury stock    
   method...............................        --         --       2,317
                                           
Number of common shares issued and         
   stock options granted in accordance     
   with Staff Accounting Bulletin          
   No. 83 (3)...........................        --         65         711
                                           -------    -------     -------
 
Shares used in per share computation        39,921     37,600      36,394
                                           =======    =======     =======
 
Per share amounts                          $ (0.17)   $ (0.11)    $  0.14
                                           =======    =======     =======
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(1)  This exhibit presents the primary and fully diluted per share computations.
     There is no material difference in the per share amounts when applying
     either method.

(2)  Pro forma net income (loss) includes a provision for income taxes as if
     Performix, Inc. ("Performix") had been a C corporation, fully subject to
     federal and state income taxes. Prior to its acquisition by the Company,
     Performix had elected S corporation status for income tax purposes and,
     consequently, historical results as they relate to Performix do not include
     a provision for income taxes.

(3)  Common shares issued by the Company during the twelve months immediately
     preceding the initial public offering date plus the number of common
     equivalent shares which were issued during the same period pursuant to the
     grant of stock options (using the treasury stock method and offering price)
     have been included in the calculation of common equivalent shares pursuant
     to Securities and Exchange Commission Staff Accounting Bulletin No. 83.