The 1990s were dominated by three teams: Georgia Southern at the beginning and end, with some combination of Marshall and Youngstown State in between. Those three programs accounted for 8 of the 10 I-AA titles in the decade. The two other winners were Montana in 1995 and UMass in 1998. Click on each of the seasons below for more information.
| Season | I-AA vs. I-A Games | I-AA over I-A Wins | Total Teams | National Champion | Runner-Up |
|---|---|---|---|---|---|
| 1990 | 65 | 9 | 87 | Georgia Southern (4) | Nevada |
| 1991 | 52 | 8 | 92 | Youngstown State | Marshall (2) |
| 1992 | 47 | 11 | 90 | Marshall | Youngstown State |
| 1993 | 47 | 7 | 118 | Youngstown State (2) | Marshall (3) |
| 1994 | 41 | 10 | 118 | Youngstown State (3) | Boise State |
| 1995 | 42 | 7 | 119 | Montana | Marshall (4) |
| 1996 | 46 | 7 | 117 | Marshall (2) | Montana |
| 1997 | 35 | 5 | 121 | Youngstown State (4) | McNeese |
| 1998 | 47 | 6 | 122 | Massachusetts | Georgia Southern (2) |
| 1999 | 51 | 7 | 122 | Georgia Southern (5) | Youngstown State (2) |