Madden NFL 07 is the final installment in the series to appear on the Game Boy Advance. It is based closely on the previous year's version, featuring the same graphics engine and all the same game modes. Teams and rosters have been updated for the new season, and a few new mini games have been added.

Gameplay modes include exhibition games, full seasons, practice, situation set-up, Two Minute Drill, and Madden Cards collecting. The Mini Camp mode also returns, with five new mini games added: punting inside 20 yards, wide receiver catch, defensive back cover, 40 yard dash and rushing the quarterback. Most modes can again be played by two players via link cable.