| 9/1/2012 | San Diego | 14 | at | Cal Poly (9-3) | 41 | at BSky | ||
| 9/8/2012 | Western New Mexico (4-7) | 27 | at | San Diego | 34 | RMAC (D2) | ||
| 9/15/2012 | San Diego | 13 | at | Harvard (8-2) | 28 | at Ivy | ||
| 9/22/2012 | Valparaiso (1-10,1-7) | 14 | at | San Diego | 51 | |||
| 10/6/2012 | San Diego | 10 | at | Drake (8-3,7-1) | 38 | |||
| 10/13/2012 | Campbell (1-10,0-8) | 0 | at | San Diego | 44 | |||
| 10/20/2012 | San Diego | 24 | at | Jacksonville (7-4,5-3) | 7 | |||
| 10/27/2012 | Dayton (6-5,5-3) | 9 | at | San Diego | 41 | |||
| 11/10/2012 | Morehead State (4-7,3-5) | 28 | at | San Diego | 41 | |||
| 11/17/2012 | San Diego | 17 | at | Davidson (2-9,2-6) | 10 | |||
| 12/1/2012 | San Diego | 34 | at | Marist (4-7,3-5) | 10 |
| vs San Diego | vs Other Opponents | San Diego compared to OOs | |
| Record: | 3-8 | 51-59 | |
| Points Scored: | 19.27 | 27.25 | 7.98 |
| Points Allowed: | 29.36 | 27.47 | 1.89 |
| Margin: | -10.09 | -0.22 | 9.87 |
| Total Points: | 48.63 | 54.72 | -6.09 |