Instead of Mario Cards like the last two installments, the player can use a Banapassport Card to save their progress. Additionally, gameplay elements from Mario Kart 7 such as the use of gliders and underwater courses are present. Fusion Karts also have health bars when playing in Team Mode with 4 players. Cooperative or team play allows the player to gain a special power-up which transforms the player's kart into a Fusion Kart that will drive and the second player is called to control the turret and shoot unlimited amounts of Green Shells at any direction for a limited period of time. The main feature of the game is that players can now play in cooperative (with 2 players) or in teams (with 4 players), similar to Mario Kart: Double Dash!! in that a player is the driver and the second shoots items.

When the player completes a lap, lights between the game screen change color. Every circuit has a time limit of 250 seconds, and when the player is at first place their photography has a crown. Unlike the other two Arcade GP games, the goal of Grand Prix is to finish each race in 3rd or better. Like Mario Kart Arcade GP and Mario Kart Arcade GP 2, there are only six racers in each race rather than eight or twelve, with the exception of playing Versus with 2-4 players or Team Battle with 4 players where there are four racers. The player then must choose which one of three themed tracks (Toad, Mario, Don-chan) they want to play. The player can choose to play in 50cc, 100cc and 150cc, with the latter two being unlockable. The arcade operator can set whether the camera should be used or not. On some cases, the camera cannot be used, in which the player's photography is their selected character's portrait. Before starting a race, the player can take their photography and decorate it with twelve included features, such as a samurai helmet and a pirate suit. Then the player can choose between seven karts, five of them being unlockable. Unlike the other two Arcade GP releases, Time Trial is not present in the game. Grand Prix, National Battle, and multi-player modes are featured in the game.

In earlier games, 'Time Up!' was used instead. Players who do not finish receive this message and the race results screen as usual, but the process here is one second faster than the normal process. The time limit for a race is 250 seconds, if the player takes too long or 15 seconds pass after the leader finishes, this screen is displayed.

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