In Ninja the player controls the ninja as he moves horizontally across the levels. The ninja can attack enemies by using his weapon or by throwing a shuriken (throwing star) or a bomb and takes damage for been hit (which can be regained via food on the level or a health potion). Each time the ninja does any damage to an enemy or a hittable object the ninja gains experience which in turn helps the ninja gain levels. When the ninja goes up a level the player can decide to put a single point in one of the three stats that are strength (more damage for each hit), armor (less damage for ninja) and speed (faster movement and more damage with shuriken). Special moves (6 in total) are unlocked through out playing the game that, with the correct keyboard combination, allows the ninja to perform a powerful move deals more damage and/or provides more defence.
The game is split into levels, with increasingly powerful enemies and monsters, that can be accessed through a world map after completing the first level. Through the world map the player can choose the branching paths for the ninja as well as visiting markets that, with the gold collected, can buy new weapons (more powerful with each unlocked market), shuriken, bombs, and health potions.