Ninja Crusaders is viewed from a side-on perspective. The objective is to reach the end of each stage, defeat regular enemies and a boss, and continue through the invasion campaign. Stages use platforms, ladders, pits, moving hazards, and enemies that require careful timing.

Players can walk, crouch, jump, attack, and collect weapon or transformation items. The active weapon changes the ninja's attack pattern, while animal forms provide different movement or combat advantages. The game offers a one-player mode and a simultaneous two-player mode, with progression through a fixed sequence of stages and limited lives.

Learn enemy placement before rushing forward, especially around pits and moving platforms. Keep a useful weapon rather than replacing it immediately, and use transformation abilities when their movement or attack advantage suits the area.

Bosses are easier when you prioritize survival over constant attacks. In two-player mode, avoid standing on the same platform or moving into the same hazard, since both players can interfere with each other's timing.