In Shadow Puppeteer one player controls a shadow and the other player controls the main character. Their task is to help each other progress through a series of platform levels to recover stolen shadows from their hometown.

The puzzles are a mix of 2D and 3D, as the boy is free to move in any direction, while the shadow is limited to being projected on 2D surfaces and using shadows cast by objects as platforms. There are 5 different worlds and each one has distinct visuals and puzzle challenge elements.

Moving an object also moves its shadow. Similarly, moving a shadow can move the object casting it. In order to solve the puzzles, the players can also manipulate the light sources and alter the dimensions of the shadows.