Ape Escape 2, like its predecessor, is a platform game in which players control Jimmy as he catches monkeys spread across each level. Like the previous game, players control Jimmy using the left analog stick and shoulder buttons while using the right analog stick to control various Gotcha Gadgets that are unlocked as the player progresses through the game. Along with returning gadgets such as the Stun Club, Monkey Net, Super Hoop, Water Net, Slingback Shooter, RC Car, and Sky Flyer, Ape Escape 2 introduces three new gadgets; the Bananarang, which attracts monkeys with its scent, the Water Cannon, which puts out fires, and the Electro Magnet, which can be used on magnetic surfaces. The Magic Punch, a gadget from the first game unlocked in the post-game, also makes a return. New to the game is the monkey sidekick, Pipotchi, who accompanies Hikaru through most of the game. While with Jimmy, Pipotchi can give the player hints, help Jimmy reach ledges, and revive him once per life when his health is depleted.
Throughout the game, players can collect golden Gotcha Coins, which become more valuable when collected in quick succession. These coins can be spent on the Gotcha Box gashapon machine to unlock bonus material. Along with various collectibles such as concept art, music, comic strips, and fables, players can unlock three brand new minigames; Monkey Football, Dance Monkey Dance, and Monkey Climber, which can be played with up to two players. Monkey Soccer (known as Monkey Football outside of North America) is an association football game, Dance Monkey Dance is a rhythm game requiring players to match dance moves to the rhythm, and Monkey Climber is a challenging game requiring players to navigate a monkey across vines. Completing the game unlocks a New Game+ mode in which players can play as the previous game's hero, Spike (Kakeru outside of North America).