| 9/5/2009 | San Diego | 24 | vs | Azusa Pacific NAIA | 12 | Glendora CA | |||
| 9/12/2009 | San Diego | 12 | @ | N Colorado | 31 | ||||
| 9/19/2009 | Marist | 10 | @ | San Diego | 17 | Pio | |||
| 10/3/2009 | San Diego | 24 | @ | Butler | 25 | Pio | |||
| 10/10/2009 | San Diego | 48 | @ | Valparaiso | 7 | Pio | |||
| 10/17/2009 | Drake | 21 | @ | San Diego | 14 | Pio | |||
| 10/24/2009 | Jacksonville | 34 | @ | San Diego | 16 | Pio | |||
| 10/31/2009 | San Diego | 14 | @ | Dayton | 21 | Pio | |||
| 11/7/2009 | Davidson | 34 | @ | San Diego | 27 | Pio | |||
| 11/14/2009 | San Diego | 13 | @ | Morehead St | 7 | Pio | |||
| 11/21/2009 | S Utah | 37 | @ | San Diego | 32 |