N2FL NCAA Top 25 Teams
*rankings finalized on January 5, 2006
| Rank | Team | W-L | AP Poll | USA Today | Previous Game Results |
| 1. | Texas | 13-0 | 1 | 1 | def. USC 41-38 in the Rose Bowl |
| 2. | USC | 12-1 | 2 | 2 | lost to Texas 38-41 in the Rose Bowl |
| 3. | LSU | 11-2 | 6 | 5 | def. Miami (Fla.) 40-3 in the Peach Bowl |
| 4. | Penn State | 11-1 | 3 | 3 | def. Florida State 26-23 (3OT) in the Orange Bowl |
| 5. | Ohio State | 10-2 | 4 | 4 | def. Notre Dame 34-20 in the Fiesta Bowl |
| 6. | Virginia Tech | 11-2 | 7 | 7 | def. Louisville 35-24 in the Gator Bowl |
| 7. | West Virginia | 11-1 | 5 | 6 | def. Georgia 38-35 in the Sugar Bowl |
| 8. | Alabama | 10-2 | 8 | 8 | def. Texas Tech 13-10 in the Cotton Bowl |
| 9. | Georgia | 10-3 | 10 | 10 | lost to West Virginia 35-38 in the Sugar Bowl |
| 10. | Notre Dame | 9-3 | 9 | 11 | lost to Ohio State 20-34 in the Fiesta Bowl |
| 11. | TCU | 11-1 | 11 | 9 | def. Iowa State 27-24 in the Houston Bowl |
| 12. | Oregon | 10-2 | 12t | 12 | lost to Oklahoma 14-17 in the Holiday Bowl |
| 13. | Florida | 9-3 | 12t | 16 | def. Iowa 31-24 in the Outback Bowl |
| 14. | Wisconsin | 10-3 | 15 | 15 | def. Auburn 24-10 in the Capital One Bowl |
| 15. | Auburn | 9-3 | 14 | 14 | lost to Wisconsin 10-24 in the Capital One Bowl |
| 16. | Miami (Fla.) | 9-3 | 17 | 18 | lost to LSU 3-40 in the Peach Bowl |
| 17. | UCLA | 10-2 | 16 | 13 | def. Northwestern 50-38 in the Sun Bowl |
| 18. | Boston College | 9-3 | 18 | 17 | def. Boise State 27-21 in the MPC Computers Bowl |
| 19. | Texas Tech | 9-3 | 20 | 19 | lost to Alabama 10-13 in the Cotton Bowl |
| 20. | Oklahoma | 8-4 | 22 | 22 | def. Oregon 17-14 in the Holiday Bowl |
| 21. | Louisville | 9-3 | 19 | 20 | lost to Virginia Tech 24-35 in the Gator Bowl |
| 22. | Clemson | 8-4 | 21 | 21 | def. Colorado 19-10 in the Champ Sports Bowl |
| 23. | Nebraska | 8-4 | 24 | 24 | def. Michigan 32-28 in the Alamo Bowl |
| 24. | Florida State | 8-5 | 23 | 23 | lost to Penn State 23-26 (3OT) in the Orange Bowl |
| 25. | California | 8-4 | 25 | 25 | def. BYU 35-28 in the Las Vegas Bowl |
| Other Notables: | Nevada (9-3) |
| Boise State (9-4) | |
| Toledo (9-3) | |
| Tulsa (9-4) | |
| Michigan (7-5) | |
| Navy (8-4) | |
| Iowa (7-5) | |