The film opens in a live-action scene with an old woman and a young girl in Central Park in New York City searching for a statue of a sled dog. The woman begins the story that happened in 1925 as the scene shifts to an animated form.
Balto a wolf-dog hybrid, shunned by both humans and dogs in the town of Nome. His only friends are Boris, a Russian goose, and Muk and Luk, two polar bears. Balto and Boris live on a grounded boat outside Nome, while Muk and Luk are occasional visitors.
One day, a dogsled race is being held. At the head end of one of the teams is Steele, a proud and fierce Siberian Husky. Balto and Boris are in Nome to watch the finish. While waiting for the teams to arrive, Balto sees a young girl named Rosy and her female husky, Jenna. He is immediately smitten by Jenna, and when Rosy loses her hat to the wind, Balto outruns the sled team and retrieves the hat to show off. However, when he tries to get closer to Jenna, Rosy's dad pulls Rosy away from him. Balto and Boris dejectedly leave town, but not before meeting Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, and Christopher Robin who have just arrived and being bullied by Steele and his companions, Nikki, Kaltag, and Star.
The night after the race, Rosy, several other children, and Christopher Robin fall ill. As Jenna worriedly watches through the hospital window, Balto approaches and attempts to flirt, but Jenna is too distressed to be receptive. Balto and Jenna enter the underfloor area of the hospital and watch the doctor give the diagnosis — Rosy (and the other children including Christopher Robin) has diphtheria, and the doctor has run out of antitoxin. An urgent request for medicine is transmitted, but sea and air routes fail and the closest rail line only goes to Nenana.
It is decided that a sled team will cover the last stretch. A race is held to determine the team members. Balto enters, and easily wins. However, he is disqualified when his heritage is revealed by Steele. That night, the team, led by Steele, sets out to Nenana and picks up the medicine; however they get lost on the way back and knock out the musher. The team now has no way home.
The news reaches Nome. Balto decides to set out on a rescue mission, accompanied by Pooh, his friends, Boris, Muk, and Luk. On the way, they are attacked by a large grizzly bear, but (with Jenna's unexpected help) are able to escape. However, Jenna is injured, and Balto orders Boris and the bears to take her home. Pooh and Rabbit decide to go with Balto while Piglet, Tigger, and Eeyore go back with Jenna, Boris, and Muk and Luk. Balto and the two friends eventually find the team and offer to help them get home. Seemingly having gone crazy, Steele does not want help, and a dogfight ensues which ends with Steele plunging down a cliff (he is apparently uninjured) without Balto having attacked once. Even with his mentally deranged state, Steele manages to make it on top of the cliff and creates a false trail to throw Balto off course. Balto takes up the lead, but soon finds that Steele tampered with the trail markers Balto left on the way and becomes lost. Eventually the crate containing the medicine becomes untied and falls off a cliff. Balto catches it, but the ground gives way underneath him and both him and the crate drop into the abyss.
Balto wakes up at the bottom of the cliff, believing that he has failed. A large white wolf appears to him, and he turns away in shame. However, as the wolf walks away, Balto notices the intact crate nearby. He realizes that being part wolf is a strength, not a weakness, and embraces that heritage with a howl, joined by the white wolf. Afterward, Balto manages to drag the crate back up the cliff to the waiting team. They are quickly on their way again, Balto using his sense of smell to figure out which marks are his and which are Steele's.
After overcoming several near-catastrophes, Balto makes it back to Nome in time to save the children and Christopher Robin, guided by a light pattern provided by Jenna. Steele (who had told the other dogs that Balto died) is revealed to be a liar and is deserted. Piglet, Tigger, Eeyore, Boris, Muk, Luk, and Jenna (all of whom thought Balto, Pooh, and Rabbit was lost) are overjoyed, and the town which once shunned Balto gives him a hero's welcome.
Returning to the present, the old woman and the girl read the statue's plaque lauding the courage and fidelity of the sled dogs that prevented the tragedy in Nome. After the woman explains that the trek is now honored with the annual Iditarod Trail Sled Dog Race that uses the same route the dog team relay took, the girl runs off playing sled dog with her own dog. Alone for a minute, the woman, who is actually Rosy, says "Thank you Balto, I would have been lost without you."
- Christopher Robin joins Pooh and his friends, but gets sick in both versions of this film.
- This was the last film DisneyAnimeManiac made before her YouTube account was suspended.
- DisneyAnimeManiac's original version was a PAL film with PAL bits from Pooh's Grand Adventure: The Search For Christopher Robin and Piglet's Big Movie and NTSC bits from The Many Adventures of Winnie the Pooh, The Tigger Movie, Winnie the Pooh: A Very Merry Pooh Year, and Pooh's Heffalump Movie. However, Daniel Esposito's upcoming remake version will be an NTSC film with NTSC bits from Winnie the Pooh and a Day for Eeyore, The Tigger Movie, The Book of Pooh: Stories from the Heart, Winnie the Pooh: A Very Merry Pooh Year, Pooh's Heffalump Movie, and Winnie the Pooh and PAL bits from The Many Adventures of Winnie the Pooh, Pooh's Grand Adventure: The Search for Christopher Robin, Piglet's Big Movie, Winnie the Pooh: Springtime with Roo, and Pooh's Heffalump Halloween Movie.
- Pooh and his friends will see Balto, Jenna, Boris, and Muk and Luk again and face Steele again in Winnie the Pooh Returns to Alaska.
- Both Winnie the Pooh and Steele were voiced by Jim Cummings.
- The TV show The New Adventures of Winnie the Pooh was in reruns on ABC Saturday mornings at the time when Balto was released in theaters in 1995.
- Yru17 originally planned to remake this remake this film, but he never watched DisneyAnimeManiac's original version of the film due to it being a PAL film and he is more used to NTSC than PAL, so Yru17 decided to let Daniel Esposito remake this film instead.