| 9/5/2009 | Southern Illinois 28 @ Marshall 31 | |
| 9/19/2009 | Southwest Baptist 7 @ Southern Illinois 59 | |
| 9/26/2009 | N Dakota St 14 @ Southern Illinois 24 | † |
| 10/3/2009 | Southern Illinois 30 @ Western Illinois 10 | † |
| 10/10/2009 | Illinois St 23 @ Southern Illinois 43 | † |
| 10/17/2009 | Southern Illinois 27 @ Northern Iowa 20 | † |
| 10/24/2009 | Youngstown St 8 @ Southern Illinois 27 | † |
| 10/31/2009 | Southern Illinois 33 @ Indiana St 0 | † |
| 11/7/2009 | Southern Illinois 34 @ S Dakota St 15 | † |
| 11/14/2009 | Missouri State 24 @ Southern Illinois 44 | † |
| 11/21/2009 | Southern Illinois 42 @ SE Missouri St 24 | |
| 11/28/2009 | Eastern Illinois 7 @ Southern Illinois 48 (FCS Playoff round 1) | |
| 12/5/2009 | William & Mary 24 @ Southern Illinois 3 (FCS Quarterfinals) |