The player controls one of the characters within the Narutimate Ninja Heroes anime and manga. The simple goal is to fight the opposing character and to win by reducing their health to zero. Along with the various weapons available to the characters also have their various special abilities taken straight from the series.
To use these attacks, however, the player must have the required chakra as indicated by the "chakra bars" located under the players health. Using the technique drains the chakra bar which can be regained through various methods, including special, character specific methods for some characters. These special techniques are not performed in real-time, however; once successfully executed, a cinematic takes place, where the player either has to fill a bar to a specific level or hit buttons illustrated in the corner of the screen faster than their opponent to assure the attack is at its full strength.
The first two games of the Narutimate Ninja Heroes series let players execute three different secret technique attacks using three different Chakra levels two different signature techniques, and a wide variety of kicks and punches. However, in Narutimate Ninja Heroes, players are only allowed to use one secret technique attack, besides the other attacks and techniques.
The game features an arcade style story mode. Although the game loosely covers the events in the original manga from the Introduction arc, the game's twelve stories are meant to depict the events from different characters' perspectives and as the result some of them deviates from the original source