Starting with the 2006 season, the NCAA renamed I-A and I-AA to Football Bowl Subdivision (FBS) and Football Championship (FCS), respectively. Despite the name change, there were only a few team changes and one conference change in place for the 2006 season.
2006 FCS Over FBS Victories (7)
- Montana State @ Colorado, 19-10
- Portland State @ New Mexico, 17-6
- Richmond @ Duke, 13-0
- New Hampshire @ Northwestern, 34-17
- Southern Illinois @ Indiana, 35-28
- North Dakota State @ Ball State, 29-24
- Cal Poly @ San Diego State, 16-14
Appalachian State (14-1 Overall, 7-0 Southern Conference) made it two I-AA/FCS titles in a row by defeating Massachusetts (13-2 Overall, 8-0 Atlantic 10 Conference) 28-17. It was the third title game appearance for the Minutemen.
The Pioneer Football League scrapped their North and South divisions for the 2006 season.
Austin Peay left the Pioneer Football League to become an FCS independent. Northern Colorado decided to leave the Great West Conference to join the Big Sky Conference.
The NCAA did not have North Dakota State, Northern Colorado, South Dakota State, and UC Davis as fully eligible for the 2005 season. Northern Colorado and UC Davis would become fully eligible starting in 2007 while NDSU and SDSU were eligible in the 2008 season. Thus, they were not counted as official teams but we do list them since they were all in their transition to I-AA.
Two other teams were in their first year of a transition and would be eligible starting in 2010 according to the NCAA. The first was Central Arkansas, moving up from Division II independent status. The second was Winston-Salem State who would complete three years of the D-II to FCS process, but decided to return to Division II and never was fully eligible per the NCAA.
We count both schools as FCS teams and in the FCS versus FBS games and upsets. For Winston-Salem State, it is a moot point: they competed in the MEAC but never faced an FBS opponent in those four seasons.
The FCS playoff format remained the same for the sixth straight season with the seeding of only the top four teams and the use of campus sites through the semifinals. The National Championship was played on December 15 at Finley Stadium in Chattanooga, Tennessee for the tenth season in a row.