The goal of the game is to maneuver the Polar Express through a maze of tracks and pick up various objects along the tracks. These objects include the Hero Boy, a special passenger car for the Hero Boy, the Hero Boy's ticket and two other passenger cars. There are various crossing all over the maze which players can click to switch the train onto a different track.
There are also various obstacles the train must avoid, which include crossings that are switched against it and caribou on the track. The player starts out with three lives and loses a live each time they run into an obstacle. After the player collects the two other passenger cars, the exit tunnel will open and the train can go through it. Attempting to go through the gate while it is closed will result in one life being lost.
According to the instructions, the game has an extra level where players can collect jewels and coal inside the tunnel. That level can be unlocked by entering a code from special The Polar Express-marked Post cereals, including The Polar Express cereal itself, but since these cereals had these markings for a limited time only, unlocking the level is practically impossible.