The game has 80 playable characters and 7 only support characters (81 playable characters and 7 support characters in Full Burst) The fighting system has been deleted, with the Sleeping Mode, a state that gave each character the same abilities when their health was full, being possible to be used at anytime after a fight, for certain characters. As in the previous games, the player can choose two characters to assist the player character in battle. The assisting characters now can also aid the playable one through the use of thirteen different types of combos. There is a new addition in the Team Attack System as the player can now use their support characters to get ready to charge and attack. Additionally, the assistants have health bars, losing health whenever they get hit, ultimately being unusable when their health bars deplete. If the player has one support character, it has ten health bars. If the player has two support characters, each has five health bars. Several arenas have become interactive, making the player automatically lose a fight if they leave a specific area.
The story mode is similar to that of Naruto Shippuden: Ultimate Ninja Storm 2 rather than the previous game Naruto Shippuden: Ultimate Ninja Storm Generations as it features boss battles that include quick time events and require the use of strategies to defeat the opponent. It also includes the “Ultimate Decision Mode” which gives the option to change the result of the battles.
Additionally, the game has mob battles in which the player controls a single character that has to battle a series of enemies.