On Christmas Eve of the late 1950s, a young boy living in Grand Rapids, Michigan, questions his belief in Santa Claus. While sleeping, he hears a noise outside and goes outside to look, where he meets the Trimaxian Adventure Crew, led by Logan. Together, they discover a train called the Polar Express, which stops in front of the boy's house where a Conductor tells them that it is headed to the North Pole.
Once aboard, the gang encounters other children, including a young girl and a know-it-all. The train stops again at another house for a young boy named Billy, who at first refuses to get on, but as the train starts to leave he attempts to board, but is unsuccessful. The boy applies the emergency brake so Billy can board the train. When Logan, his friends, and the children are given hot chocolate, the girl hides and saves a cup for Billy who is riding in the observation car. The conductor helps her deliver it. The boy and Logan discover that she left her ticket on the seat. They attempt to bring it to her but loses it in the wind while passing between carriages. The girl returns to find the ticket missing and the boys tell the conductor that they lost it.
The conductor takes the girl up to the train's roof. The protagonists finds that the ticket has flown back into the train, grabs it and, with a select few of Logan's crew, climb onto the train's roof to give the ticket to the girl but arrive to see the light of the conductor's lantern vanish in the darkness. They cross along the train's roof until they meet a hobo, who claims to be the owner of the Polar Express and king of the North Pole. The hobo offers the group some coffee, as the Boy expresses doubt that Santa exists. With that, the hobo replies that if he is seen, the boy actually believes in Santa (Though Logan believes otherwise). The hobo then helps the gang follow the conductor and girl. They ski down the train roof as it approaches Flat Top Tunnel. When the hobo claims that the tunnel's clearance is low, the boy and his friends hop in the engine as the hobo disappears.
The group and the boy find that the girl is driving the train while Steamer, the engineer and Smokey, the fireman, try to fix the train's headlight. They are forced to stop when a herd of caribou block the tracks. The conductor gets the caribou to move by pulling Smokey's beard, making him yell. The train continues with the conductor, Logan, his friends, and the children stuck in the front of the engine. The cotter pin of the throttle slips out during an attempt to slow down the train due to the train accelerating dangerously as it approaches and rides along Glacier Gulch. The train soon reaches a lake that has risen and frozen over the tracks. However, the lost cotter pin pierces the ice and it begins to crack, putting everybody in danger. Smokey immediately repairs the throttle with a spare, and the conductor orders the train to full-speed to get the train to the other side of the lake. They do so and the train runs back to normal just before the ice is completely broken up. During which, the boy hands back the girl's ticket for the conductor to punch.
Having arrived at the North Pole, the gang and two children find Billy alone in the observation car, but Hero Boy accidentally uncouples it, causing it to speed backwards. The car stops at a turntable, where they encounter Annabelle, one of Santa's reindeers with a surprising backstory. She agrees to lead Logan, his friends, and the children to back to the city square and together they travel from section to section in the North Pole. Finally, they make it back to the center of the city in time for Santa's appearance and sleigh preparation as well. While the sleigh is being readied, a bell falls off a harness. The boy picks it up and shakes it after remembering that the girl, Billy, Logan, and his friends could hear a bell earlier when he could not. In addition, the boy's doubts start to have an effect on Logan's friends and Logan begs for the Hero Boy to regain his faith in the Christmas Spirit. The boy finally admits his belief in the spirit of Christmas and finally hears the bell. Santa selects the boy to receive "The First Gift of Christmas", allowing the boy to choose the bell. In addition, Logan and his friends appoint their friend, Annabelle, as an honorary member of the team shortly before she departs to help Santa deliver the toys to the children of the world.
As they all prepare to head home, the conductor takes their tickets and punches an individual message for each of them (For example "Learn", "Depend, Rely, and Count On", "Lead", and "Believe" for Know-It-All, Billy, the girl, and the boy respectively). Once aboard, the boy discovers that the bell has fallen through a hole in his pocket and before Logan and his crew can act, the train already departs. Although at first saddened by the loss, he soon cheers up when Billy is dropped off home, where he gets word from Billy that Santa already visited his house. The boy arrives home and the Conductor wishes him a Merry Christmas, the Trimaxian Adventure Team and the kids wave goodbye to him, and the hobo appears on the top roof of the train, waving goodbye to the boy as he disappears into the winter snow one final time.
On Christmas morning, the boy's sister, Sarah, finds a small present hidden behind the Christmas tree. The boy opens the present and discovers that it is the bell, which Santa found. When the boy rings the bell, both he and Sarah marvel at its beautiful sound. Hoever, their parents neither believe in Santa Claus nor the spirit of Christmas and do not hear it and remark it to be broken. In the film's last line, as Logan and his crew discover from a book during their departure, the boy narrates the conclusion of his story decades later, reciting the book's final line:
"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."
- This is the first Logan's Adventures story to take place in a computer animated movie.