The 2013 edition of the NCAA college football series contains a number of enhancements and improvements to the gameplay. There are over 400 new catches and pass animations, less occurrence of blind swats, and the ability to abort the play after the snap. After hiking the ball one of the 20 new dropbacks is used and when going too far the pocket is broken. For passes, button icons now show the awareness of receivers, for instance in gray when he is still on his way or not looking. Then one of the 25 new pass trajectory zones is used, compared to just one in the previous edition. There are also return kicks and punts. In certain game modes a new feature called Reaction Time can be activated. Holding down a trigger is then used to slow the game, providing more time to make decisions.

Returning from the previous edition is the Road to Glory career mode starting with a custom, new player or coach in high school. Players eventually move on to colleges and coaches can accept or decline offers, starting out as an offensive coordinator, a defensive coordinator or a head coach. Through the online options new high schools can be added and the names (high schools, teams, colours, stadiums) can be customized. Matches have studio scorecard updates, an ESPN ticker at the bottom of the screen, and voices sideline reports. There are three new NCAA Football Bowl Subdivision (FBS) teams: Massachusetts (UMass), Texas–San Antonio (UTSA), and Texas State, and the game incorporates some rule changes for the 2012-2013 season of NCAA Division I (A) FBS games.

The quick play game modes consist of exhibition, practice, coach a game, mascot mash up, and button mode. In the career modes there is an online Dynasty mode (single-player or multiplayer) next to Road to Glory. Entirely new for this edition is the Heisman Challenge. It is similar to Road to Glory, but players select one of ten former Heisman winners and after a video interview get to control the player on his real team at that time, even though that can be customized. Different for Heisman compared to Road to Glory is a list of goals shown in the top-right corner of the screen. To win this mode these major goals need to be achieved. Players are at their maximal abilities and have maximal coach trust in the senior year, making available play changes and calls. If a challenge is completed that player is unlocked in any game mode, including Road to Glory and the ability to transfer him to Madden NFL 13's Superstar mode. Exporting draft classes to Madden NFL was removed in this version of the game.