On Christmas Eve, a young boy is hoping for belief in the true spirit of Christmas. He suddenly hears a noise from downstairs and runs to investigate. Seeing a shadow of what appears to be Santa Claus, he soon discovers that it is his parents. He runs back to his room and looks through magazines and encyclopedias for confirmation of Santa Claus and the North Pole, but to no avail. Hearing his parents coming, he runs back to bed and pretends to be asleep while his parents whisper about how he had once stayed up late listening for Santa Claus. About an hour after they leave, a fantasy magic train called the Polar Express pulls up in front of his house. He is invited aboard by the train's mysterious conductor to journey to the North Pole. Though he initially hesitates, he boards the train after it starts to move.
On the train, the boy encounters a group of other children who are on their way to see Santa Claus, including a young girl, a know-it-all, and a lonely little boy. The boy also encounters a mysterious hobo, who lives on the top of the train, as well as the engineer and fireman. They must all overcome a variety of obstacles; at one point, a herd of caribou blocking the tracks. Later, the cotter pin holding the throttle together breaks. The train, now out of control and with the Hero Boy, Hero Girl and Conductor standing on the front, then reaches "Glacier Gulch," an area with steep downhill grades. The three must hold on tightly as the train speeds through Glacier Gulch and onto a frozen lake. The train tracks are frozen under the ice, and as a result, the conductor must guide the engineer and the fireman towards the other side of the lake as the ice breaks up behind them.
They then reach the North Pole and find out that the lonely boy named Billy, riding alone in the observation car, does not want to see Santa because he comes from a broken home on the bad side of his hometown and says that Christmas does not work out for him. The boy and girl run back to try to get him to come along with them, but the Boy accidentally steps on the uncoupling lever and the car speeds back. The three of them travel from section to section of the North Pole's industrial area, first visiting the Control Center, then the Wrapping Hall, and finally a warehouse before they are airlifted back to the center of the city via air ship. As they watch the final preparations, one bell falls off Santa's sleigh. The boy picks it up and shakes it, remembering that the girl could hear a bell earlier when he could not. As before, he can not hear it. The boy then says he believes in Santa and the spirit of Christmas. He then sees Santa's reflection on the bell; he shakes the bell again and hears it at last. He gives the bell back to Santa.
The boy is handpicked by Santa Claus to receive "The First Gift Of Christmas". Realizing that he could choose anything in the world, the boy asks for the beautiful-sounding silver bell (that only believers can hear) which fell from Santa's sleigh. The boy places the bell in the pocket of his robe and all the children watch as Santa takes off for his yearly delivery.
The children return to the train, and the conductor punches letters into each ticket. These letters spell some form of advice (such as "Learn," "Lead," or "Believe" for the Know-it-All, Hero Girl, and Hero Boy respectively). As the train leaves, the Hero Boy discovers the pocket of his robe torn and the bell missing. His friends suggest they go back outside to find it, but the train was already departing. He is saddened by the loss of his bell, but is happy when he sees that Santa had already visited Billy; as he is holding up his present at his doorway. When the train arrives at Hero Boy's house, he says his goodbyes to all of his friends, and waves from the doorway of his home as the train pulls away. On Christmas morning, his sister Sarah finds a small present hidden behind the tree after all the others have been unwrapped. The Boy opens the present and discovers that it is the bell, which Santa had found on the seat of his sleigh. When the boy rings the bell, both he and his sister marvel at the beautiful sound; but because their parents no longer believe in Santa Claus or Christmas, they do not hear it. The last line in the movie repeats the same last line from the book:
- "At one time, most of my friends could hear the bell, but as years passed, it fell silent for all of them. Even Sarah found one Christmas that she could no longer hear its sweet sound. Though I've grown old, the bell still rings for me, as it does for all who truly believe."