On Christmas Eve, a boy witnesses a train called the Polar Express that is about to depart for the North Pole. When the boy examines the engine, the conductor lets him board the train. The boy meets other children, including a girl and a know-it-all kid. When the train picks up Billy, the hero boy applies the emergency brakes. Billy initially declines to board but changes his mind. The conductor summons a waiter team, who give the children hot chocolate, and the girl stows away one cup under her seat to give to Billy, who is alone in the observation car. The girl and conductor deliver the hot chocolate cup to Billy until the hero boy discovers the girl’s ticket is unpunched. He loses it before he can return it. After the ticket is abused by the wind and animals, it slips back in the train. The girl explains her lost ticket, and the conductor considers ejecting her before taking her for a walk on the top of the train instead. The hero boy locates the lost ticket and pursues them.
Losing the girl and conductor, the boy meets a hobo, who claims he is the owner of the train and King of North Pole. Desperate to find the girl, the hobo helps the boy by skiing down the rooftops. Before reaching Flat Top Tunnel, the boy jumps into the engine’s coal tender and finds the girl is controlling the train. After the driver, Steamer, and his aide, Smokey, replace the light, Steamer witnesses something unusual ahead and orders the train to be stopped. The hero boy applies the brakes and the engine on the train screeches to a halt. When the conductor witnesses a caribou crossing, he pulls Smokey’s beard, causing him to let out animal-like sound effects, and the caribou horde clear out. The train continues on but starts to speed up, when the cotter pin of the throttle sheers off causing the train to run out of control. Moving at extreme speed, the train becomes a roller coaster as it crosses Glacier Gulch and enters a frozen lake. The lost cotter pin pierces the ice, causing it to crack. Smokey uses his hairpin to repair the throttle. As the ice cracks, the conductor sends Steamer to the other side of the tracks before the icy lake shatters completely. The hero boy returns the girl’s lost ticket for the conductor to punch. The conductor takes the two kids to a room with abandoned toys. The hobo scares the hero boy with an Ebenezer Scrooge puppet, and the boy retreats to the observation car where the girl and Billy are singing. The trio sees auroras, and the train finally reaches the North Pole.
Upon arrival, kids form lines while the hero boy and girl see Billy depressed and alone in the observation car. They encourage Billy to go, but the carriage is uncoupled after the hero boy accidentally stepped on the latch, rolls downhill backwards, and stops on a turntable. The trio explore the city’s industrial area until falling on a pile of presents, which are transported in a giant bag carried by a blimp. The gargantuan bag is placed on Santa’s sleigh, and elves remove the kids. As the reindeer are prepared, Santa arrives. One bell breaks loose from a harness, and the hero boy retrieves it. He first hears nothing, but when he believes, he hears a sound. Santa entrusts the boy the bell as “The first gift of Christmas”. Santa leaves with his reindeer, and a band plays in celebration.
The elves re-attach the lost observation car back to the train, and the kids prepare to head home. The kids request the hero boy show the bell, but when he is devastated to learn that he has lost it; he regains his spirit after Billy is taken home. The hero boy is taken home and everyone else bids him farewell. The next morning, the boy’s sister wakes him up to open presents, including the bell he lost. The parents hear nothing, and the boy leaves it on the table. The narrator ends the story by saying the bell only rings for those who truly believe.