| 9/3/2016 | Western New Mexico (3-8) | 0 | at | San Diego | 27 | RMAC (D2) | ||
| 9/10/2016 | San Diego | 16 | at | Cal Poly (7-5) | 38 | at BSky | ||
| 9/24/2016 | Dayton (9-2,7-1) | 22 | at | San Diego | 34 | |||
| 10/1/2016 | San Diego | 44 | at | Butler (4-7,2-6) | 10 | |||
| 10/8/2016 | Davidson (2-9,0-8) | 3 | at | San Diego | 52 | |||
| 10/15/2016 | San Diego | 38 | at | Drake (7-4,6-2) | 7 | |||
| 10/22/2016 | Valparaiso (4-7,3-5) | 10 | at | San Diego | 49 | |||
| 10/29/2016 | San Diego | 27 | at | Marist (5-6,5-3) | 3 | |||
| 11/12/2016 | Stetson (4-7,2-6) | 7 | at | San Diego | 42 | |||
| 11/19/2016 | San Diego | 57 | at | Campbell (5-5,3-4) | 21 | |||
| 11/26/2016 | San Diego | 35 | at | Cal Poly (7-5) | 21 | at BSky | ||
| 12/3/2016 | San Diego | 7 | at | North Dakota State (12-2) | 45 | 1AA Playoffs | at MVC |
| vs San Diego | vs Other Opponents | San Diego compared to OOs | |
| Record: | 2-10 | 66-56 | |
| Points Scored: | 15.58 | 28.81 | 13.23 |
| Points Allowed: | 35.67 | 27.49 | 8.18 |
| Margin: | -20.09 | 1.32 | 21.41 |
| Total Points: | 51.25 | 56.30 | -5.05 |