Over the course of the game, the player controls one of a select few characters directly based upon their counterparts in the Naruto anime and manga. Clash of Ninja is a member of the fighting game genre; the player pits their character against another character controlled by the game's AI or by another player, depending on the mode that the player is in. The objective is to reduce the opponent's health to zero using basic attacks and special techniques unique to each character that are derived from techniques they use in the Naruto anime or manga.