| 9/3/2016 | New Hampshire (8-5) | 0 | at | San Diego State | 31 | CAAF (1AA) | ||
| 9/10/2016 | California (5-7) | 40 | at | San Diego State | 45 | P12 | ||
| 9/17/2016 | San Diego State | 42 | at | Northern Illinois (5-7) | 28 | at MAC | ||
| 10/1/2016 | San Diego State | 24 | at | South Alabama (6-7) | 42 | at SBC | ||
| 10/8/2016 | UNLV (4-8,3-5) | 7 | at | San Diego State | 26 | |||
| 10/14/2016 | San Diego State | 17 | at | Fresno State (1-11,0-8) | 3 | |||
| 10/21/2016 | San Jose State (4-8,3-5) | 3 | at | San Diego State | 42 | |||
| 10/28/2016 | San Diego State | 40 | at | Utah State (3-9,1-7) | 13 | |||
| 11/5/2016 | Hawaii (7-7,4-4) | 0 | at | San Diego State | 55 | |||
| 11/12/2016 | San Diego State | 46 | at | Nevada (5-7,3-5) | 16 | |||
| 11/19/2016 | San Diego State | 33 | at | Wyoming (8-6,6-3) | 34 | |||
| 11/26/2016 | Colorado State (7-6,5-3) | 63 | at | San Diego State | 31 | |||
| 12/3/2016 | San Diego State | 27 | at | Wyoming (8-6,6-3) | 24 | |||
| 12/17/2016 | Houston (9-4) | 10 | vs | San Diego State | 34 | Las Vegas Bowl | AAC |
| vs San Diego State | vs Other Opponents | San Diego State compared to OOs | |
| Record: | 3-11 | 76-86 | |
| Points Scored: | 20.21 | 31.06 | 10.85 |
| Points Allowed: | 35.21 | 31.81 | 3.40 |
| Margin: | -15.00 | -0.75 | 14.25 |
| Total Points: | 55.42 | 62.87 | -7.45 |