Baku Baku Animal is a game where Master Piggy's pupil, Polly, competes in a contest to become the Royal Zookeeper. The King initially refuses, but the Minister tells him that his daughter wants a pet and needs help caring for it. A three-part challenge of skill and daring is set up to select the perfect zookeeper.
Baku Baku Animal features three different play modes: practice, normal, and hard. It also allows for two-player competition against each other (except on the Sega Master System). The main objective is to pair animal heads with their corresponding food items – rabbit heads with carrot tiles, dog heads with bones, panda heads with bamboos, and monkey heads with bananas.
Baku Baku Animal includes a bonus item called the "BB coin" that can appear at random, removing piles of tiles from the playfield. These removed tiles will then be sent to the opponent's playfield, increasing the difficulty level. Polly must navigate through this challenge to win and become the Royal Zookeeper.