As with the original Ninja-Kid, the goal of each stage is to defeat the many enemies roaming around by first reaching them and then throwing ninja stars at them. Ninja-kun can also acquire scrolls that briefly give him stronger attacks, like a fire burst that takes out all nearby enemies.

Each stage (or "scene") has a different layout, with some being merely a single screen (such as Scene 1) as well as larger vertically- and horizontally-scrolling stages. The enemies are usually different too, with increasing difficulty.