Captain Toad: Treasure Tracker builds upon the Adventures of Captain Toad minigame within Super Mario 3D World, where the basic gameplay model had been first introduced. In the game, players control Captain Toad, or sometimes his companion Toadette, who must safely navigate through various obstacles in order to reach a gold star at the end of each level.
The player can manipulate the camera to view around the level, which can reveal hidden areas containing bonus items. Captain Toad can be hit twice before dying, and can collect mushrooms to restore his health. As in Super Mario 3D World, Captain Toad is able to walk and run, but unable to jump. Toad can pull up plants from the ground, which yield either coins to be collected or turnips to be thrown at enemies. He can collect a pickaxe that, similar to the hammer found in Donkey Kong, briefly allows him the ability to clear out enemies and obstacle blocks. The game makes use of the Wii U GamePad’s features, as the player can touch the screen to manipulate platforms, as well as use gyroscopic controls to aim turnips while riding mine carts.The game makes use of Amiibo figurines.