| Rank | Coach | Games | Penalties | Penalty Yards | Penalties Per Game | Penalty Yards Per Game |
|---|
| 1 | Chad Lunsford | 49 | 232 | 1,899 | 4.73 | 38.76 |
| 2 | Willie Fritz | 24 | 119 | 1,135 | 4.96 | 47.29 |
| 3 | Dell McGee | 1 | 5 | 45 | 5.00 | 45.00 |
| 4 | Clay Helton | 26 | 141 | 1,263 | 5.42 | 48.58 |
| 5 | Jeff Monken | 54 | 314 | 2,774 | 5.81 | 51.37 |
| 6 | Kevin Whitley | 8 | 48 | 401 | 6.00 | 50.13 |
| 7 | Frank Ellwood | 11 | 69 | 576 | 6.27 | 52.36 |
| 8 | Brian VanGorder | 11 | 71 | 615 | 6.45 | 55.91 |
| 9 | Chris Hatcher | 33 | 222 | 1,996 | 6.73 | 60.48 |
| 10 | Mike Sewak | 49 | 330 | 2,776 | 6.73 | 56.65 |
| 11 | Erk Russell | 106 | 739 | 6,695 | 6.97 | 63.16 |
| 12 | Tim Stowers | 74 | 520 | 4,493 | 7.03 | 60.72 |
| 13 | Paul Johnson | 72 | 521 | 4,547 | 7.24 | 63.15 |
| 14 | Tyson Summers | 18 | 136 | 1,183 | 7.56 | 65.72 |