<PAGE>
 
                                                                   EXHIBIT 11.01

                       AMISYS MANAGED CARE SYSTEMS, INC.
                      COMPUTATION OF EARNINGS  PER SHARE
                       (IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>
                                                                 THREE MONTHS ENDED          NINE MONTHS ENDED     
                                                                   SEPTEMBER 30,               SEPTEMBER 30,       
                                                                                                                   
                                                                  1996           1995       1996          1995     
                                                                  ----           ----       ----          ----     

<S>                                                             <C>           <C>         <C>             <C>       
Net income                                                      $   1,217     $     987   $   3,024       $     822
                                                                =========     =========   =========       ========= 
                                                                                                                    
Weighted average Class A common  shares outstanding                    --     4,800,000          --       4,800,000 
                                                                                                                   
Weighted average common shares outstanding                      7,565,000       450,000   7,565,000         450,000 
                                                                                                                   
Common shares issued within one year of initial public                 --        75,000          --          75,000
 offering                                                                                                          
                                                                                                                   
Options issued during the first quarter  of 1996                    3,200            --          --              --
                                                                                                                   
Options issued during the second  quarter of 1996                  43,400            --          --              -- 
                                                                                                                   
Weighted average options exercised during the                                                                      
 period                                                            42,858                    41,068              -- 
                                                                                                                   
Weighted average shares issued during  secondary offering          75,500            --      32,790              -- 
                                                                                                                   
Stock options issued within one year of                                --            --          --              -- 
 initial public offering  (using the treasury stock                                                                
 method and the initial public offering price of $14.50                                                            
 per  share)                                                           --       574,950          --         574,950 
                                                                                                                   
Stock options issued (using treasury stock method and                                                              
the average price of $22.56 and $21.78 per share for              510,922            --     506,518              -- 
the periods presented, respectively)                           ----------    ----------  ----------      ----------
                                                                                                                    
Weighted average number of common  shares outstanding           8,240,880     5,899,950   8,145,376       5,899,950 
                                                               ==========    ==========  ==========      ========== 
                                                                                                                    
Net income per common share and common                          $     0.15    $    0.17  $     0.37       $    0.14
 share equivalent                                              ==========    ==========  ==========      ========== 
 </TABLE>

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