Mickey and Minnie return to Game Boy Advance with the release of Disney's Magical Quest 2, which originally appeared on 16-bit systems under the title, The Great Circus Mystery (1994). Players once again control either Disney character as they embark on a mission to stop the mischievous Pete, who has disrupted the local circus and is working with a trio of cronies known as the Mice Brothers. Following the same format introduced in Disney's Magical Quest, this sequel features lighthearted platform action across six themed worlds, beginning with the circus and continuing through jungles, ice, mountains, and more.

The costume-changing element of the first game is here as well, with Mickey or Minnie able to acquire a Sweeper, Ranger, and Cowboy outfit to help players defeat enemies or to cross hazardous terrain. The Sweeper costume lets characters vacuum up small enemies and coins as well as activate switches or move objects. The Ranger costume involves climbing and sliding down ropes to scale steep cliffs, while the Cowboy costume comes equipped with a wooden horse so characters can gallop along the ground at high speeds. Multiplayer features are once again supported via Game Link Cable, this time featuring both competitive and cooperative action.