HarmoKnight is a side-scrolling rhythm platformer starring Tempo, a young boy from the planet Melodia. When aliens attack the planet and kidnap Princess Ariana, it's up to Tempo and his friends to save their world and princess. Along with Tempo, the player may sometimes need to take control of the archer Lyra or the drum-and-cymbal-playing duo of Tyko and Cymbi, each of whom have slightly different playing styles.
Regardless of which playable character is used, the basic gameplay mechanics are the same. Each level is set to a music track, and automatically scrolls. Every action the player takes adds instrumentation to the background music, with more successful actions producing richer sounds. As such, playing well is the only way to hear the level's music in full. The player needs to collect music notes, hit instruments as they appear, attack enemies, and dodge obstacles. Failing to perform the latter two tasks will result in the loss of a heart. If the player loses all their hearts, the level is failed.
The game is composed of 54 main levels spanning 8 worlds, and 5 extra levels featuring music from the Pokémon series of RPGs, which share a developer with HarmoKnight. Longer levels may feature one or more checkpoints.