| 9/1/2012 | Central Conn (2-8) | 17 | at | Stony Brook | 49 | NE | ||
| 9/8/2012 | Pace (0-9) | 7 | at | Stony Brook | 77 | NE10 (D2) | ||
| 9/15/2012 | Stony Brook | 17 | at | Syracuse (8-5) | 28 | at BigE | ||
| 9/22/2012 | Colgate (8-4) | 31 | at | Stony Brook | 32 | Pat | ||
| 9/29/2012 | Stony Brook | 23 | at | Army (2-10) | 3 | at Ind | ||
| 10/6/2012 | Charleston Southern (5-6,3-3) | 7 | at | Stony Brook | 49 | |||
| 10/13/2012 | Stony Brook | 27 | at | Coastal Carolina (8-5,5-1) | 21 | |||
| 10/20/2012 | Gardner-Webb (3-8,2-4) | 10 | at | Stony Brook | 41 | |||
| 10/27/2012 | Stony Brook | 56 | at | Presbyterian (2-9,0-6) | 17 | |||
| 11/3/2012 | VMI (2-9,1-5) | 7 | at | Stony Brook | 45 | |||
| 11/10/2012 | Stony Brook | 14 | at | Liberty (6-5,5-1) | 28 | |||
| 11/24/2012 | Villanova (8-4) | 10 | at | Stony Brook | 20 | FCS Round 1 | CAAF | |
| 12/1/2012 | Stony Brook | 10 | at | Montana State (11-2) | 16 | FCS Round 2 | at BSky |
| vs Stony Brook | vs Other Opponents | Stony Brook compared to OOs | |
| Record: | 3-10 | 62-74 | |
| Points Scored: | 15.54 | 26.36 | 10.82 |
| Points Allowed: | 35.38 | 30.21 | 5.17 |
| Margin: | -19.84 | -3.85 | 15.99 |
| Total Points: | 50.92 | 56.57 | -5.65 |