| 09/02/06 | at | Iowa | 7-41 |
| 09/09/06 | hosting | South Dakota St | 36-7 |
| 09/23/06 | hosting | Sacramento St | 59-14 |
| 09/30/06 | at | Portland St | 26-20 |
| 10/07/06 | at | Eastern Washington | 33-17 |
| 10/14/06 | hosting | Northern Arizona | 24-21 |
| 10/21/06 | at | Weber St | 33-30 |
| 10/28/06 | hosting | Idaho St | 23-10 |
| 11/04/06 | hosting | Cal Poly SLO | 10-9 |
| 11/11/06 | at | Northern Colorado | 53-21 |
| 11/18/06 | hosting | Montana St | 13-7 |
| 11/25/06 | hosting | McNeese St | 31-6 |
| 12/02/06 | hosting | Southern Illinois | 20-3 |
| 12/08/06 | hosting | Massachusetts | 17-19 |