The game received 'favorable' reviews according to the review aggregation website Metacritic. Not unlike many other games, there are various differences across regions when the game (and its following sequels) was releasing worldwide. At that time, he thought of the idea for Frog Hop, which became one of the first games to be made for Rhythm Heaven. Tsunku really liked the idea of the Flick action regardless of the long time to adapt. The Flick action took them about 'two to three months' to research and 'six months' to eventually adapt the control into the game. The Flick action took the staff a 'little getting used to' as they had to make it feel 'fair' to the player until they realised that if flicking was combined with the music it would give the players a 'good sense of timing'. The ability to touch the edge of the Touch Screen was considered, but was determined to be too difficult.

Osawa didn't like the idea of using buttons, so he considered a control mechanic that involved the Touch Screen. The game's development 'wasn't easy' for the staff. The conception of the game is credited to Nintendo programmer Kazuyoshi Osawa who previously worked on Metroid and WarioWare titles. Rhythm Heaven was developed by Nintendo SP&D1 with the assistance of Tsunku, a music record producer, both also worked on the original Rhythm Tengoku. The European version has been fully translated in Spanish, English, French, German, and Italian language, including the vocal songs in the Fan Club, The Dazzles, Frog Hop, Karate Man, and Airboarder Rhythm Games. Soundtrack albums for the game have been released in Japan, but not in North America. There were plans to include the Japanese songs in the music player section, but they were soon taken out due to space restrictions. These vocals were re-recorded in English for the Western version by other vocalists (most notably Ayaka Nagate, a former member of the Tsunku-produced Coconuts Musume), as were some of the voice cues. Rhythm Heaven uses original music composed by Tsunku and Masami Yone, with vocals by TNX artists including Canary Club, The Possible, and Tsunku himself (credited as Occhama ). While the game is automatically set to be played on right-handed mode, there is also a left-handed mode for left-handed individuals. Completing a Perfect run earns more bonus features in the cafe, such as song sheets and lyrics. Only appearing on the menu three times before moving elsewhere, these runs require the player to complete a Rhythm Game perfectly without making any mistakes. Sometimes, a Rhythm Game that a player has received a Superb rating on may be randomly selected for a Perfect attempt. By receiving a 'Superb' rank on each Rhythm Game, players receive Medals which unlock bonus content, such as Endless Games, Rhythm Toys and Guitar Lessons. 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 2, 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.

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