| 08/31/06 | hosting | Stephen F. Austin | 45-7 |
| 09/09/06 | at | Brigham Young | 24-49 |
| 09/16/06 | hosting | North Texas | 28-3 |
| 09/23/06 | at | Navy | 24-23 OT |
| 10/03/06 | hosting | Southern Miss | 20-6 |
| 10/14/06 | at | East Carolina | 31-10 |
| 10/21/06 | at | Memphis | 35-14 |
| 10/27/06 | hosting | UTEP | 30-20 |
| 11/04/06 | at | Houston | 10-27 |
| 11/11/06 | hosting | Rice | 38-41 |
| 11/18/06 | at | SMU | 24-34 |
| 11/24/06 | hosting | Tulane | 38-3 |
| 12/23/06 | hosting | Utah | 13-25 |