Madagascar: Operation Penguin is a sequel to the game Madagascar and features the movie's penguins as the main characters. Your goal is to help the animals escape from the Central Park Zoo in New York City via underground tunnels. As Private Penguin you use silly weapons to attack and travel throughout the world. Once you complete a level, you open up a portion of a tunnel for the penguins to travel through.

The game is a side-scrolling platformer mainly geared towards children. Besides learning new abilities through items, your goal is also to collect items in each level.