"Castle of Dr. Brain" features a point-and-click mode of gameplay and three levels of difficulty, which the player can change at any time. The player can also change the pointer from a hand, which will interact with puzzles, to an eye, which will give information about an object, occasionally leading to clues to help solve puzzles. Typically, pointing the hand or the eye at an object that is not a puzzle will give a joke about it. The game also features Hint Coins, which the player earns by solving puzzles and can use for assistance on puzzles with which they are having difficulty.