In Big Brain Academy, tests are done to measure the player's brain's mass. The heavier the brain, the smarter the brain is or the better its reaction time. There is no single game mechanism to Big Brain Academy; as it is an assortment of puzzles with no one puzzle having greater priority than the other. Correct answers add to the brain mass, while incorrect answers reduce the brain mass. The better the player does, the more difficult the puzzles become.
There are three modes of play: Test mode, Practice mode, and Versus mode.