The game is split into two parts: one resembles a RPG, featuring various locations that Endou and his team have to explore in order to get new items, face several other players in short casual battles or to advance further in the story. Most of the goals of this part are indicated by a giant purple arrow; the second part is the actual match: using the stylus, the player moves the soccer team around against another team. The player can dodge opponent's attacks, slide tackle to take the ball away, or use a special ability available to the characters they recruited. The result of any of his players actions are determined by seven skills, the player's affinity, and the total number of players participating in an action. Special abilities can only be stopped with other abilities, meaning that they will always win against basic tactics. Shoot and catch hissatsu however play simultaneously, which means that unlike defending the ball they always consume the Ability bar and at the beginning are determined by the player affinity only.
New to this game are Shoot Chain Hissatsu. Shoot chains allow a player with a hissatsu meeting the right requirements to use a to increase the power of another shoot by standing in front of the ball and using a hissatsu of their own. Also new to Inazuma Eleven 3 are Hissatsu Tactics. Hissatsu Tactics are a type of team hissatsu that have various effects. Finally, with The Ogre, Tournaments have been introduced. These are a small series of matches that take place among the story team and various other random teams.