Players had the option to play through a full 11-game season (or less as desired) as any of the 108 selectable Division I-A teams before the team advances to one of the college bowl games. College Football USA 96 would mark the first and the only time that the Southwest Conference would appear in a college football video game because it would merge with the Big 8 to form the Big 12 the following year. It also marked the only time that the University of Pacific Tigers football team would appear in a video game, as they dropped their football program after the 1995 season to save money.

Players could select from 400 plays, and could choose one of five receivers on each play using the new passing mode. The game added other features and options such as: four-player mode, three possible lengths for a game, substitutions, injuries, fake snaps, spins, audibles, interceptions, hurdles, dives, blocked kicks, and laterals.