| 09/02/06 | hosting | Portland St | 6-17 |
| 09/09/06 | at | New Mexico St | 34-28 |
| 09/16/06 | hosting | Missouri | 17-27 |
| 09/23/06 | hosting | UTEP | 26-13 |
| 09/30/06 | at | Air Force | 7-24 |
| 10/07/06 | hosting | Wyoming | 10-14 |
| 10/14/06 | at | UNLV | 39-36 |
| 10/19/06 | hosting | Utah | 34-31 |
| 10/28/06 | at | Colorado St | 20-19 |
| 11/11/06 | hosting | TCU | 21-27 |
| 11/18/06 | at | Brigham Young | 17-42 |
| 11/25/06 | hosting | San Diego St | 41-14 |
| 12/23/06 | hosting | San José St | 12-20 |