<PAGE>
 
                                                                      EXHIBIT 11

                       PAYMENTECH, INC. AND SUBSIDIARIES
                                        
                      COMPUTATION OF NET INCOME PER SHARE
                THREE MONTHS ENDED SEPTEMBER 30, 1997 AND 1996
                 (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)


<TABLE> 
<CAPTION> 
                                                                           THREE MONTHS ENDED
                                                                              SEPTEMBER 30,
                                                                       ---------------------------
                                                                           1997            1996
                                                                       -----------     -----------
<S>                                                                    <C>             <C>
Primary                                                                             
-------                                                                             
Net income (loss)..............................................        $     4,172     $    (3,284)
                                                                       -----------     -----------
Weighted average common equivalent shares outstanding                               
      Average common shares outstanding........................         35,258,197      31,703,181
      Common stock equivalents -- stock options................            194,184         420,578
                                                                       -----------     -----------
      Weighted average common and common stock                                           
         equivalent shares.....................................         35,452,381      32,123,759
                                                                       ===========     ===========
                                                                                       
Net income (loss) per share....................................        $      0.12     $     (0.10)
                                                                       ===========     ===========
Fully diluted                                                                                     
-------------
Net income (loss)..............................................        $     4,172     $    (3,284)
                                                                       -----------     -----------
Weighted average common and common equivalent                                          
      shares outstanding                                                                           
      Average common shares outstanding........................         35,258,197      31,703,181
      Common stock equivalents -- stock options................            195,417         455,745
                                                                       -----------     -----------
      Weighted average common and common stock                                         
         equivalent shares.....................................         35,453,614      32,158,926
                                                                       ===========     ===========
                                                                                       
Net income (loss) per share assuming full dilution.............        $      0.12     $     (0.10)
                                                                       ===========     ===========
</TABLE>