The Missouri Fox Trotter is one of the oldest breeds of horses  developed in the United States. As early as the 1820's new settlers in the Missouri Territory started crossing their best mares to the Thoroughbreds, Morgans, and Arabians that other settlers to the territory had brought with them. Of the resulting colts and fillies, the most famous "family groups" were the Brimmer, Diamond, and Fox strains. These horses were used for every purpose from pleasure riding, all-round farm work, and racing. When religious groups within Missouri were able to put an end to horse-racing activities, breeders produced a new type of horse with a smooth gait that could travel long distances and great periods of time over rough ground.

This new horse eventually became known as the Missouri Fox Trotter, especially after the introduction of Saddlebred blood in the mix resulted in the gait that is known as the "fox trot."  A Fox Trotter  walks with its front legs and trots with its rear legs so that the hind hooves slide right into the track of the front feet. This gait is what has made the fox trotter famous for its comfortable ride. In addition to the fox trot, the Fox Trotter  can do a  Four-Time Walk, in which the hind feet overstep the track of the front feet. This gait is similar to that of the Tennessee Walking Horse. The third gait of the Missouri Fox Trotter is the standard canter. Unlike the Tennessee Walking Horse and Saddlebred, the Fox Trotter does not step high( also termed "break above level"), and it is usually shown in Western tack, not a cutback saddle usually associated with English pleasure show classes.

The official Missouri Fox Trotter Stud Book was formed in 1948, and the popularity of the breed blossomed rapidly thereafter. By 1978 there were 15,000 horses registered with the Stud Book.