Unlike The Golden Compass for consoles and PC, The Golden Compass for the Nintendo DS is a 2D platformer with 3D graphics. It follows the events of the movie, over more than 40 levels, controlling Lyra, her dæmon Pan, and the armored polar bear Iorek. Pan can transform into one of four different animals, which are useful for combat and puzzle-solving. Each level can be played in one of 3 difficulties, with previous levels replayable at any time. Collectibles are hidden in the levels, and can be used to upgrade Iorek's armor.

Multiplayer (Single-cart download or multi-cart) is included, based on the Alethiometer from the movie. By moving the needles, see how close you got to your opponent's symbols. Find your opponent's symbols before they find yours. Finally, an Alethiometer to just play around with is included.