| 09/02/06 | at | South Florida | 10-41 |
| 09/09/06 | hosting | West Virginia Tech | 76-0 |
| 09/23/06 | at | Toledo | 7-41 |
| 09/30/06 | hosting | South Dakota St | 17-20 |
| 10/07/06 | hosting | Southern Utah | 30-27 |
| 10/14/06 | hosting | Texas St-San Marcos | 17-27 |
| 10/21/06 | at | Stephen F. Austin | 20-17 |
| 10/28/06 | at | Sam Houston St | 31-18 |
| 11/04/06 | hosting | SE Louisiana St | 34-13 |
| 11/11/06 | at | Northwestern St | 29-26 |
| 11/18/06 | hosting | Nicholls St | 26-10 |
| 11/25/06 | at | Montana | 6-31 |