The game is fundamentally the same as the first one; players take control of Mark and his team in an overworld collecting items, improving stats at training points and partaking in random encounters. Scouting and recruiting players has been moved to the Inazuma Bus, where players can contact Coach Hillman to search for people by name or other criteria. The connection map is also located on the bus, in the form of a small machine at the front.

The main hub of the game is the aforementioned Inazuma Bus, where players can restore their FP and TP, as well as travel to other regions of Japan. The game contains nine regions to explore in total, each with its own story arc and set of players to collect. These regions are unlocked as the story progresses.

The matches are also near identical to the first game; players control their team with the stylus, and initiate a command duel when they run into the opposition. The result of the player's actions in a duel is determined by their form (which is decided by their stats, element, and the total number of players participating in the duel). It's possible for the player to call a time-out mid-match to plan movements, fire-up to boost their performance, or charge quickly forward at the cost of FP (Fitness Points).

Special abilities return, which can be used in place of basic maneuvers at the cost of TP (Technical Points), but can now be developed and get stronger the more they are used. Mega Moves are also introduced, which are incredibly powerful but have a high TP cost.

Two other mechanics introduced to matches in Inazuma Eleven 2 are "long-distance shooting" and "blocking". At any time during a match, the player can tap the "S" button at the top-right of the screen, causing whoever has the ball to automatically shoot, no matter where they are on the pitch. Also, if a special move is marked with an "L", then they can use that move when shooting this way. Likewise, if a player has a special move marked with a "B", then they can intercept the opposing team's shots if they are within range, either powering them down or stopping them entirely.

Another new mechanic introduced in this game is "alter-egos". Before a match begins, some characters can have their characteristics, stats, and special moves switched to a different set if they have an alter-ego. For example, one of the new characters introduced in this game, Shawn Frost, is usually a defender with a high "Guard" stat and blocking moves, but has an alter-ego which is a striker with a high "Kick" stat and shooting moves.

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