The last season of the decade saw the end of some programs and the resumption of an old program.
2009 FCS Over FBS Victories (5)
- Villanova @ Temple, 27-24
- Richmond @ Duke, 24-16
- William & Mary @ Virginia, 26-14
- New Hampshire @ Ball State, 23-16
- Central Arkansas @ Western Kentucky, 28-7
Villanova (14-1 Overall, 7-1 Colonial Athletic Association) won a close affair 23-21 over Montana (14-1 Overall, 8-0 Big Sky Conference) in their first and only (to date) FCS Championship Game appearance. It was a second consecutive loss for the Grizzlies in the title game.
There were no conference changes in effect for the 2009 season.
Iona decided to end their football program after the 2008 season when they were an FCS independent. Two other FCS independent teams joined conferences for the 2009 season – Bryant went into the Northeast Conference and Marist went to the Pioneer Football League.
Old Dominion decided to bring back their football team and were classified as an FCS independent for the 2009 season.
The NCAA did not list Bryant (2012), Central Arkansas (2010), North Carolina Central (2011), North Dakota (2012), Presbyterian (2011), South Dakota (2012), or Winston-Salem State (2011) as eligible FCS teams in 2009. We count those programs as FCS teams for the 2009 season.
The FCS playoff format remained the same for the ninth and final 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 18 at Finley Stadium in Chattanooga, Tennessee for the 13th straight season. It was the last FCS title game played in Chattanooga to date.