Set in late eighteenth- and early nineteenth-century Vermont, the story follows a boy named Joel Goss and his lifelong bond with a small, reddish-brown colt called Little Bub, who later becomes famous as Justin Morgan.
Joel, a thin, straw-haired boy in worn clothes, accompanies his schoolmaster, Justin Morgan, on a journey of over 100 miles on foot from Randolph, Vermont, to Springfield, Massachusetts. Morgan, a graying singing teacher, hopes to collect a debt owed by Farmer Beane. Two colts graze in Beane's meadow: a large colt named Ebenezer and a smaller one called Little Bub. Joel is immediately drawn to the little colt. Beane confesses he cannot repay the debt and offers Ebenezer as payment instead. Joel begs to have Little Bub come along too, but Morgan refuses, calling the colt undersized. The next morning, Joel sneaks out and feeds each colt an apple. Little Bub approaches cautiously, and when the colt finally accepts, a friendship is sealed. As Joel leads Ebenezer through the gate, Beane deliberately leaves it open, letting Little Bub follow. Morgan reluctantly agrees to let the small colt tag along.
The journey northward takes nearly a month. Morgan gives geography lessons, and Joel gradually accustoms Little Bub to carrying a bundle on his back, beginning the process of gentling, or taming and training a young horse. The colt proves his intelligence, sensing snakes before the others and following the sound of farmhouse conch shells to kitchens where the group receives meals. Travelers admire Ebenezer but dismiss Little Bub as a runt. Near home, they visit Hiram Hawkes, a horse trader, who declares Little Bub worthless.
Joel's mother welcomes the colts warmly, but his father, Mister Goss, is stern and unyielding. Having once owned a horse that had to be shot, he refuses to care for another and announces that Joel must be bound as an apprentice to Miller Chase, the local innkeeper and sawmill operator. Joel is devastated. That evening, Morgan tells Joel he has found a home for Ebenezer and new lodgings with the Jenks family. He asks Joel to gentle Little Bub so the colt can eventually be sold to pay Morgan's debts. Joel reluctantly agrees. The next day, Joel signs apprenticeship papers before the local Justice of the Peace, committing himself for seven years.
Joel's daily life becomes monotonous sawmill labor, but after evening school with Morgan, he races to the Jenks place to train Little Bub. He teaches the colt to wear a halter, accept a bit coated with maple syrup, pull a loaded cart, and gallop bareback across the hills. Joel trains Bub gently, preserving the colt's spirit.
This arrangement ends when Ezra Fisk, a new settler, arranges to rent Little Bub for a year. His hired man, Robert Evans, will use the horse to clear wooded land along the White River. Fisk offers 15 dollars a year plus the horse's keep. Joel is heartsick but nods his consent, understanding Morgan's need to pay his debts. One April afternoon, Evans rides a mud-coated Little Bub to Chase's millyard, where farmers hold log-pulling contests. The larger work horses have all failed to budge a massive pine log. Evans demands three men sit astride the log to increase the difficulty. Little Bub lunges into the harness and drags the log, riders and all, to the sawmill in two pulls. The stunned crowd erupts, and Joel throws his arms around the horse's neck.
Bub's fame grows. He wins pulling contest after contest until local farmers refuse to enter their animals. Nathan Nye, a local organizer, creates a quarter-mile raceway along the White River, and Little Bub wins his first race in 36 seconds. A letter then arrives from Jonathan Toppington, a wealthy New Yorker, challenging Morgan's "mongrel-bred" work horse to race against two Thoroughbreds at Brookfield for a 50-dollar purse. Morgan accepts. On race day, Joel brings a hidden hound-dog, knowing Bub despises dogs. In the first race, Joel releases the hound onto the track, and Bub chases it at full speed, winning by five lengths. The New Yorkers cry foul. In the second race, Bub throws a front shoe at the first turn but recovers to win by half a length. Morgan gives five dollars each to Joel and Evans, and Joel begins saving to buy Bub.
When the rental term expires, Morgan declines all offers from horse traders and uses Bub to travel as a singing master across mid-Vermont schools. At Woodstock, however, Morgan falls gravely ill with lung fever. Months later, Joel receives a farewell letter: Morgan has left Bub with Sheriff Rice's family to pay his medical debts, expressing hope that Joel will eventually reclaim the horse. Soon after, the schoolmaster dies.
The community gives the horse the schoolmaster's full name: Justin Morgan. He passes through a series of owners, always proving his worth. Neighbors bring mares to be bred by him, and his colts consistently inherit his qualities: a bold eye, compact body, easy gaits, and honest disposition. When the horse is eventually put up for auction, Joel rushes there with his five silver dollars, but the bidding surpasses his means. A carpenter wins at 65 dollars, only for a dark-eyed stranger to force 12 gold pieces into the carpenter's hands and ride off on Justin Morgan. The horse vanishes. For years, Joel tracks rumors across Vermont but always arrives too late.
Miller Chase promises Joel a partnership and a barn if he ever finds the Morgan. When the War of 1812 is declared against Great Britain, Joel enlists in the Vermont militia's cavalry, serving as assistant to the shoeing smith while searching for Justin Morgan among the military mounts. His unit fights at the Battle of Plattsburg, where a small American force defeats the British. Joel treats wounded horses through the night, examining every face for Justin Morgan, but does not find him.
After the war, Joel settles in Randolph as a respected young man and horse doctor. One bitter winter night, he hears a thin, high whinny carried on the wind. He races to Chase's Inn and finds six gaunt horses hitched to a freight wagon. The smallest, the near wheel horse, harnessed closest to the wagon, raises his head and swivels his tiny ears. It is Little Bub. Joel holds the horse's face and digs frozen snowballs from his hoofs. Inside the inn, he confronts the surly teamster and borrows 25 dollars from Miller Chase, who warns that the horse is old and may die. Joel replies that one does not turn down a friend because he is old.
Joel nurses the horse back to health with steaming oat mashes, rubdowns, flannel bandages, and melted sheep's fat for cracked hoofs. Within months, Justin Morgan's eyes brighten and his gaunt frame fills out. When President James Monroe visits Burlington, Vermont, Joel rides Justin Morgan in a cavalry procession. A bee forces Monroe to dismount from his own horse, and the President notices Justin Morgan's bright, intelligent face. Joel presents the horse, and Justin Morgan carries the President with steady, cadenced action to the college green, unflinching even when a gun salute shakes the earth. Afterward, townspeople swarm Joel with questions about the horse's pedigree. Joel tells the story of Farmer Beane's gift to the singing master and concludes that nobody truly knows the bloodline. Addressing Bub directly, he declares that the horse is just like them: American.