One evening as Jajamaru and Sakurahime where watching a rare meteor storm, they witnessed a UFO crash land just beyond a nearby mountain. Inside the vessel they discovered the Great Galactic King. The king claimed the evil Don Destroida had just transformed his precious star into a mechanical planet filled with fearful robots. Our heroes than decide it is up to them to save the universe from Don Destroida and his robot horde. Jajamaru and Sakurahime are granted hammers by the Great Galactic King before taking off into space with the king's ship.

In this Ninja Jajamaru-kun game, users can play either as Jajamaru or Sakurahime. Ninja Jajamaru: Ginga Daisakusen is somewhat of a departure from previous 8-bit entries in that it draws some design elements from other contemporary platformers creating a different feel when compared to older games. Character sprites are bigger and more cartoonish. Players jump on top of enemies to defeat them. A myriad of powerups can be found inside of blocks scattered across each level. A new status bar on the bottom of the screen displays various information such has remaining lives, currently active powerups, etc. In certain levels, pipes can be used to access sub-areas.

Aside from general platforming gameplay Ninja Jajamaru: Ginga Daisakusen has a somewhat unique multi-staged running mechanic dubbed the "reservoir dash." While standing still users can hold the B button to build up power. This power can then be released to run at high speed. It also allows the player to jump higher and further than normal. This is often required to make it across large gaps, or get over tall obstructions. At at full charge the character will begin somersaulting. This allows the player slice throw enemies while airborne, make jumping through hectic areas a bit easier. If the player sits and charges the reservoir dash to long the character becomes exhausted and temporarily can't move, leaving them exposed to attack. The rate at which charge is built varies between the two playable characters. Jajamaru can built up dash faster, while Sakurahime can higher jump power while dashing.