The game loosely follows the penguin's side-plot from the film, as they attempt to escape from the Central Park Zoo. Players control Private throughout a variety of 2D platforming levels. Private obtains several gadgets and objects to assist him, including: a large frozen fish to attack, a fruit slingshot, a soda bottle jet pack, a straw blowpipe, and a hamburger wrapper parachute.[1][2]
GameZone gave the game a 7.5/10, stating: "With more variety and some mini-games, this could have been a better game, but as it stands, it's still a good outing with those penguins from Madagascar".[1] Console Gameworld said it offers "witty dialogue to keep the story moving along and has some replay value." Game Chronicles claimed that Operation Penguin is "technically a very solid game, and only falls apart once you realize that [...] it's all the same old same old."[2]