Theatrhythm Final Fantasy is a rhythm video game. Players take control of four Final Fantasy characters and choose from a selection of Final Fantasy titles, from the very first Final Fantasy to Final Fantasy XIII. Each game consists of three stages: field, battle, and story. Each of these stages has different gameplay mechanics; once a stage is completed, the characters level up. The difficulty can be adjusted to suit "beginners as well as rhythm masters." Players can unlock musical and cinematic scenes as they progress through the game. Gameplay requires people to tap the correct spot on the screen in time to the music playing. The main game section, "Sequential Mode," offers 3 unique styles of each stage: Field Music, Battle Music, and Event Music, as well as the ability to play through opening and ending themes.

Field Music is a rhythm game in which the screen moves from right to left and the player must either tap a note, slide the stylus in a certain direction, or hold the stylus on the screen and follow the wavy line that appears. The goal is to reach the end of the stage before the music stops, at which point another character is waiting to give the player an item. Successful play results in the character accelerating, while a mistake causes them to fall. To increase speed, each level offers the option to ride a chocobo.

Battle Music is a simulated battle in which the player must tap notes correctly to deal damage to enemies on the screen. The goal is to kill all opponents and eventually the boss character within the allotted time while the music plays. The notes appear from left to right. In this mode, players must tap a note, swipe the stylus in a certain direction, or hold the stylus on the screen for a long note. Good timing results in the characters' attacks being more powerful, and can also activate special abilities. The player is allowed one summon attack per battle.

A Story Music scene features one or more scenes from the selected Final Fantasy title, which play on the background screen. Character stats and abilities, other than health, have no effect on these stages.