In present day at New York City, an elderly woman and her granddaughter are walking through Central Park, looking for a memorial statue. As they seat themselves for a rest, the grandmother tells a story about Nome, Alaska, back in 1925 which shifts the film from live-action to animation.
Balto, a wolfdog hybrid, lives on the outskirts of Nome with his best friend and adoptive father, a snow goose named Boris and two polar bears, Muk and Luk. Being half-breed, Balto is ridiculed by dogs and humans alike. His only friend in town is a red husky named Jenna who Balto has a crush on and is challenged by the town's favorite sled dog, Steele, a fierce and arrogant purebred Alaskan Malamute.
That night, all the children, including Jenna's owner, Rosie, began to get sick with diphtheria. Severe winter weather conditions prevent medicine to be brought by air or sea, and the closest rail line ends in Nenana, Alaska. The next day, a dog race is held to determine the best-fit dogs for a sled dog team to get the medicine. Balto enters and wins, but Steele stomps on his paw, causing Balto to growl in pain and bare his teeth, resulting in him being disqualified. The team departs that night with Steele in the lead and picks up the medicine successfully, but on the way back, conditions deteriorate and the disoriented team ends up stranded at the base of a steep slope with the musher knocked unconscious. When the word reaches Nome, Balto sets out in search of them with Boris, Muk and Luk. On the way, they are attacked by a huge grizzly bear, but Jenna, who followed their tracks, arrives to help, though she is injured in the process. The bear pursues Balto out onto a frozen lake, where it falls through the ice and drowns; Balto himself narrowly avoids the same fate with Muk and Luk's help. However, Jenna's injuries mean that she cannot make the journey with the rest of the group. Balto instructs Boris, Muk, and Luk to take her back to Nome while he continues on alone.
Balto eventually finds the team, but Steele refuses his help and a fight ensues, ending with Steele falling off a cliff. Balto takes charge of the team, but Steele, refusing to concede defeat, throws them off the trail and they lose their way again. While attempting to save the medicine from falling down a cliff, Balto himself falls.
Back in Nome, Jenna has told the other dogs about Balto's rescue which makes them laugh. Steele appears and tells everyone about the deaths of the members of the team, he also tells them about Balto's accident. Although the other dogs do believe Steele's story, Jenna knows he is lying. Jenna, also, believes that Balto will be back with the medicine.
When he regains consciousness, he is ready to give up hope, but when a large, white wolf appears and he notices the medicine crate still intact nearby, he realizes that his part-wolf heritage is a strength, not a weakness, and drags the medicine back up the cliff to the waiting team. Using his advanced senses, Balto is able to filter out the false markers Steele created. After encountering further challenges, Balto and the sled team finally make it back to Nome with only one vial lost. A pity-playing Steele is exposed as a liar and is abandoned by the other dogs. Reunited with Jenna and his friends, Balto earns respect from both the dogs and the humans. He visits Rosie who thanks him for the medicine.
Back in the present in New York City, the elderly woman and her granddaughter finally find the memorial commemorating Balto, and she explains that the Iditarod trail covers the same path that Balto and his team took from Nenana to Nome. The woman, who is actually Rosie, looks up at the statue and repeats the same line, "Thank you, Balto. I would have been lost without you," before walking off to join her granddaughter as the sun shines upon the Balto statue.