The first decade of the new millennium ended up with quite a bit of parity akin to the 1980s decade. The 1980s saw 8 different I-AA champions while the 2000 through 2009 seasons saw the same number. In addition, there was only one repeat winner: Appalachian State when they won three straight from 2005 through 2007. 2005 was the final season of the two subdivisions being referred to as I-A and I-AA. Starting with the 2006 season, the NCAA renamed them to Football Bowl Subdivision (FBS) and Football Championship Subdivision (FCS), respectively.
| Season | I-AA vs. I-A Games | I-AA over I-A Wins | Total Teams | National Champion | Runner-Up |
|---|---|---|---|---|---|
| 2000 | 56 | 15 | 123 | Georgia Southern (6) | Montana (2) |
| 2001 | 57 | 8 | 123 | Montana (2) | Furman (2) |
| 2002 | 65 | 8 | 123 | Western Kentucky | McNeese (2) |
| 2003 | 71 | 10 | 121 | Delaware | Colgate |
| 2004 | 55 | 6 | 119 | James Madison | Montana (3) |
| 2005 | 54 | 2 | 120 | Appalachian State | Northern Iowa |
| 2006 | 78 | 7 | 122 | Appalachian State (2) | Massachusetts (2) |
| 2007 | 78 | 9 | 122 | Appalachian State (3) | Delaware (2) |
| 2008 | 87 | 2 | 125 | Richmond | Montana (4) |
| 2009 | 94 | 5 | 125 | Villanova | Montana (5) |