NCAA Football 99 was the sixth edition of the game. The game featured University of Michigan cornerback and Heisman Trophy winner Charles Woodson on the cover. It's tagline read Desire+Pride=Victory!.

The game featured all 112 Division I-A teams and the ability to create or edit players and names, sixty fight songs and crowd chants. Over eighty historical teams were added to the game as well. The Heisman Memorial Trophy is replaced by the 'EA Sports MVP" trophy and other awards are given out. Recruiting is simple and done in a serpentine draft system. The Rose Bowl, Cotton Bowl, Fiesta Bowl and Sugar Bowl are playable, the other Bowls played have EA Sports as the sponsor. Created players from this game can be imported to the title Madden NFL 99. It featured no commentary by booth announcers, instead a PA Announcer provides the commentary. Also, unlike the current games in this franchise, NCAA Football 99 featured an optional 16 team playoff at the end of the season in dynasty mode.