| 9/7/2013 | Thiel (3-7) | 20 | at | Juniata | 41 | TPAC | ||
| 9/14/2013 | Juniata | 37 | at | Dickinson (3-7,3-6) | 14 | |||
| 9/21/2013 | Gettysburg (4-6,3-6) | 16 | at | Juniata | 38 | |||
| 9/28/2013 | Juniata | 16 | at | Franklin & Marshall (7-4,6-3) | 46 | |||
| 10/5/2013 | Johns Hopkins (10-1,9-0) | 65 | at | Juniata | 10 | |||
| 10/19/2013 | Juniata | 28 | at | Ursinus (7-3,6-3) | 7 | |||
| 10/26/2013 | Muhlenberg (8-3,7-2) | 27 | at | Juniata | 7 | |||
| 11/2/2013 | Juniata | 42 | at | McDaniel (2-8,2-7) | 21 | |||
| 11/9/2013 | Juniata | 27 | at | Moravian (2-8,2-7) | 14 | |||
| 11/16/2013 | Susquehanna (1-9,1-8) | 10 | at | Juniata | 17 | |||
| 11/23/2013 | Juniata | 34 | at | Albright (8-3) | 45 | ECAC Southwest Bowl | at MIDAC |
| vs Juniata | vs Other Opponents | Juniata compared to OOs | |
| Record: | 4-7 | 51-52 | |
| Points Scored: | 25.91 | 28.54 | 2.63 |
| Points Allowed: | 27.00 | 27.17 | -0.17 |
| Margin: | -1.09 | 1.37 | 2.46 |
| Total Points: | 52.91 | 55.71 | -2.80 |