Ninja Jajamaru-kun must rescue his beloved Princess Sakura from a fiendish catfish-faced pirate in a realm of feudal Japanese folklore. He begins on the bottom of a three-tiered horizontal field, where he can break weak brick ceilings by jumping into them.
As Ninja Jajamaru-kun progresses through levels, he must defeat two enemies on each tier to clear the level. Enemies can be killed with shuriken, which is the only weapon available without a power-up. However, some enemies need to be stunned or killed by falling into a hole in a tier or being jumped on. If Ninja Jajamaru-kun touches an enemy projectile or body, he will instantly die.
After defeating an enemy, its spirit will ascend, and the player can grab it for extra points. At 80 seconds remaining in each stage, Princess Sakura will drop a cherry blossom onto the field, which will float through platforms until intercepted by Ninja Jajamaru-kun. Collecting three blossoms triggers a bonus stage, where the Pirate Lord throws fire down on Ninja Jajamaru-kun.
The game features increasingly difficult bonus stages with clones of the Pirate Lord and more fire. New enemies based on Japanese folklore appear at each level, with a new boss enemy that is more intelligent than the others. The boss will eventually become a standard minion after several stages, but a new more difficult boss will appear to replace it.
Items can be found by breaking brick ceilings or picking them up, and they have temporary effects on Ninja Jajamaru-kun's status. These items include:
Speed-up: Increases Ninja Jajamaru-kun's speed.
Ninja-cart: A carriage that can crush enemies and move at high speeds.
Shuriken: Increases the distance of Ninja Jajamaru-kun's shuriken throws.
Invisibility Potion: Makes Ninja Jajamaru-kun invisible or invincible.
Inscribed Coins: Gives additional points, with different colors giving different point valuations.
Extra Ninja: Extra lives, very rare.
Bombs: Can appear when a ceiling is cracked open, but beware of getting killed by them.
Trusty Frog: Appears with three items or four lives, and can provide additional benefits.