On Christmas Eve in the late 1950s, 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 allows him to board the train. The boy meets other children, including a girl and a know-it-all boy with a Brooklyn accent and a hyperactive personality. When the train picks up another boy, Billy, the hero boy applies the emergency brakes when Billy initially declines to board. The conductor summons a waiter team to give the children hot chocolate and the girl hides one under her seat to give to Billy. The girl and conductor go to deliver the hot chocolate cup to Billy, but the hero boy discovers the girl’s ticket is unpunched. He loses it before he can return it. The boy explains the lost ticket to the conductor, and the conductor takes her for a walk on the top of the train. The hero boy locates the lost ticket and pursues them.
The boy meets a hobo, who claims he is the owner of the train and King of North Pole. He helps the boy by skiing down the rooftops as the Polar Express goes down a steep slope like a roller coaster. 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 engine’s headlight, Steamer sees something unusual ahead and orders the train to be stopped; the cause is a big herd of caribou on the track. The hero boy applies the brakes and the engine on the train screeches to a halt. The conductor pulls Smokey’s beard several times, causing him to let out animal-like sound effects, and the caribou horde moves away. Afterwards, the cotter pin of the throttle sheers off causing the train to speed up and run out of control it crosses Glacier Gulch at dangerous speeds before derailing onto a frozen lake. The lost cotter pin falls off the train and pierces the ice, causing it to crack. Smokey uses his hairpin to repair the throttle and they manage to get the train back under control. The conductor sends Steamer to “steer” the train to the tracks on the other side before the train falls through the ice. The hero boy returns the girl’s lost ticket for the conductor to punch. The conductor takes the two kids to a train car where are many abandoned toys. The hobo scares the hero boy with an Ebenezer Scrooge puppet, and the boy retreats to the observation car. The train encounters auroras, and finally reaches the North Pole.