There was more movement in and out of the I-AA level to end the final season of the millennium.
1999 FCS Over FBS Victories (7)
- Western Illinois @ Northern Illinois, 27-21
- Northern Iowa @ Ohio, 36-21
- Troy @ Cincinnati, 31-24
- Buffalo @ Connecticut, 23-0
- Troy @ Middle Tennessee, 48-31
- Furman @ North Carolina, 28-3
- Hofstra @ Buffalo, 20-13
Georgia Southern (13-2 Overall, 7-1 Southern Conference) ended the decade in a familiar place: as I-AA champs. It was their fifth since 1985 after they defeated Youngstown State (12-3 Overall, 5-1 Gateway Conference) with a crushing 59-24 victory.
There were only two minor changes at the conference level. The SWAC split into East and West divisions while also instituting a conference championship. The Atlantic 10 Conference scrapped the unequal two divisions starting with the 1999 season.
Two teams decided to leave I-AA with Buffalo joining the MAC after previously being an I-AA independent and Middle Tennessee left the Ohio Valley Conference to become an I-A independent team. Western Kentucky, from I-AA independent status, replaced Middle Tennessee in the OVC.
Replacing the two newly departed teams at the I-AA level were Albany and Stony Brook from the Division II Eastern Football Conference. They both became members of the Northeast Conference.
Two final changes were Saint John’s (NY) leaving the Metro Atlantic Athletic Conference (MAAC) to become I-AA independent for a season while La Salle did the opposite as they jumped into the MAAC.
The I-AA playoffs remained the same for the fifth consecutive season. The NCAA seeded all 16 teams playoffs and they also kept campus sites through the semifinals. The National Championship was played on December 18 at Finley Stadium in Chattanooga, Tennessee for the third year in a row.