To clear a Rhythm Game and progress onto the next game, the player needs to get a 'Just OK' or 'OK' rank. In each Rhythm Game, the player must attempt to keep with the rhythm throughout the level, receiving a rank at the end of the game depending on how well they did. The game's fifty Rhythm Games are split into ten sets, each consisting of four Rhythm Games and a themed Remix level that incorporates the previous games (or more) into one song. A guitar-based minigame late in the game known as Rockers, along with the unlockable guitar lessons, also include the use of the DS's shoulder buttons to bend guitar notes. Controls used include tapping the touch screen, holding the stylus down on the touch screen, dragging it across the screen and flicking it off the screen. Throughout the game, players use the stylus to play through several rhythm-based levels known as Rhythm Games, each with their own specific rules.

Unlike its predecessor which is played using the GBA's buttons, Rhythm Heaven is played using the touch screen with the DS held vertically, similarly to a book.