Schedule:
| Game | Date | Away Team (Rank) | Away Score | Home Team (Rank) | Home Score | Game Status | Result | Margin |
|---|---|---|---|---|---|---|---|---|
| 1 | 2016-09-03 | Western New Mexico | 0 | San Diego | 27 | Final | W | 27 |
| 2 | 2016-09-10 | San Diego | 16 | Cal Poly | 38 | Final | L | -22 |
| 3 | 2016-09-24 | Dayton | 22 | San Diego | 34 | Final | W | 12 |
| 4 | 2016-10-01 | San Diego | 44 | Butler | 10 | Final | W | 34 |
| 5 | 2016-10-08 | Davidson | 3 | San Diego | 52 | Final | W | 49 |
| 6 | 2016-10-15 | San Diego | 38 | Drake | 7 | Final | W | 31 |
| 7 | 2016-10-22 | Valparaiso | 10 | San Diego | 49 | Final | W | 39 |
| 8 | 2016-10-29 | San Diego (148) | 27 | Marist (203) | 3 | Final | W | 24 |
| 9 | 2016-11-12 | Stetson (228) | 7 | San Diego (143) | 42 | Final | W | 35 |
| 10 | 2016-11-19 | San Diego (144) | 57 | Campbell (225) | 21 | Final | W | 36 |
| 11 | 2016-11-26 | San Diego (145) | 35 | Cal Poly (147) | 21 | Final | W | 14 |
| 12 | 2016-12-03 | San Diego | 7 | North Dakota State | 45 | Final | L | -38 |