This ranking is comprised of the top 25 college football programs based on an average of their teams' final ratings from 1990-1999.
| Rk | Team | W | L | T | Rating |
|---|---|---|---|---|---|
| 1 | Florida State | 109 | 13 | 1 | 0.8216 |
| 2 | Florida | 102 | 22 | 1 | 0.7739 |
| 3 | Nebraska | 108 | 16 | 1 | 0.7702 |
| 4 | Tennessee | 98 | 22 | 3 | 0.7566 |
| 5 | Michigan | 93 | 26 | 3 | 0.7502 |
| 6 | Penn State | 97 | 26 | 0 | 0.7363 |
| 7 | Ohio State | 91 | 29 | 3 | 0.7047 |
| 8 | Washington | 82 | 35 | 1 | 0.6930 |
| 9 | Notre Dame | 84 | 35 | 2 | 0.6907 |
| 10 | Alabama | 91 | 31 | 1 | 0.6852 |
| 11 | Miami (Florida) | 92 | 27 | 0 | 0.6820 |
| 12 | Colorado | 87 | 29 | 4 | 0.6803 |
| 13 | Texas A&M | 94 | 28 | 2 | 0.6522 |
| 14 | UCLA | 69 | 46 | 0 | 0.6118 |
| 15 | Southern California | 68 | 49 | 4 | 0.6118 |
| 16 | Syracuse | 82 | 35 | 3 | 0.6086 |
| 17 | Auburn | 72 | 40 | 3 | 0.6056 |
| 18 | Kansas State | 87 | 30 | 1 | 0.6039 |
| 19 | Georgia | 72 | 43 | 1 | 0.5950 |
| 20 | Virginia | 78 | 40 | 1 | 0.5894 |
| 21 | Virginia Tech | 77 | 39 | 1 | 0.5861 |
| 22 | Arizona | 71 | 46 | 1 | 0.5787 |
| 23 | Oregon | 70 | 48 | 0 | 0.5759 |
| 24 | Brigham Young | 86 | 39 | 2 | 0.5759 |
| 25 | North Carolina | 78 | 39 | 1 | 0.5674 |
Minimum for inclusion: Participation in 6 ranked seasons.