2003 marked the end of several programs from several different conferences while the usual conference skipping was also in effect.
2003 FCS Over FBS Victories (10)
- Florida Atlantic @ Middle Tennessee, 20-19
- Western Illinois @ Eastern Michigan, 34-12
- Cal Poly @ UTEP, 34-13
- Eastern Washington @ Idaho, 8-5
- Stephen F. Austin @ Louisiana-Monroe, 23-21
- Villanova @ Temple, 23-20
- Colgate @ Buffalo, 38-15
- Northwestern State @ Louisiana-Monroe, 14-10
- Idaho @ Montana, 41-28
- Delaware @ Navy, 21-17
Delaware (15-1 Overall, 8-1 Atlantic 10 Conference) won their first I-AA title in their second appearance after losing the 1982 Championship game. The Blue Hens shut out Colgate (15-1 Overall, 7-0 Patriot League) 40-0.
There were no conference changes in effect for the 2003 season.
Four teams decided to end their football programs. Canisius, Fairfield, and Saint John’s (NY) all dropped their programs after the 2002 season. Morris Brown was in the middle of a transition to the I-AA level, but they too decided to cut the football program.
Coastal Carolina started a new program and immediately joined the Big South Conference. Southeastern Louisiana decided to restart its program after having last played in 1985. They were I-AA independent upon their return.
Elon and VMI both swapped conferences with Elon going from the Big South to the Southern Conference while VMI did the opposite. Two teams joined the Ohio Valley Conference: Jacksonville State from the Southland Conference and Samford (previously I-AA independent).
The duo of UC Davis and Northern Colorado were both in their first year of a transition to I-AA from the Division II level. Both schools left the Division II North Central Conference.
The NCAA Handbook does not count the Division II duo of UC Davis and Northern Colorado until their first year of eligibility in 2007. We count them as I-AA since they were in transition. However, both teams played a mix of I-AA and Division II opponents and ultimately do not add to the I-AA/FCS versus I-A/FBS game totals during the transition.
The I-AA playoff format remained the same for the third 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 19 at Finley Stadium in Chattanooga, Tennessee for the seventh season in a row.