Super Dot Jump is a retro-style action platformer. The game contains 100 single-screen levels, divided into ten worlds. In the first world, simple, rectangular blocks comprise the platforms, which the player must use to reach a star which advances the player to the next level. Each new world introduces new platforms, such as one which the player must move, and one that explodes.

Super Dot Jump takes place in the alien city of Vrta, located below the surface of the moon. For a long time, the citizens of Vrta have been disappearing. Due to the disappearances, one alien named Urtu decided to leave Vrta to travel the galaxy, searching for the missing aliens.