Fort Duchesne was established by Major Frederick William Benteen on 20 August 1886, on a site selected by General George Crook, and General Crook soon took command of the new fort. Construction began in October 1886 and the reservation was officially designated by President Cleveland in September 1887. The fort continued to serve, with an average detachment of 250 men, until its closure in September 1912. Remnants of the fort still exist.

Fort Duchesne was established to replace Fort Thornburgh in the Uinta Basin, which had been abandoned by the U.S. Army during the winter of 1884-85. An outbreak of inter-band warfare among the Utes during the winter of 1885-86 once more raised the question of placing a fort in the basin. The Department of the Interior and the War Department each sent investigators to the area who recommended the establishment of a permanent fort. Crook selected the site in August 1886; it was three miles above the junction of the *Uintah and Duchesne rivers and midway between the Whiterocks agency and Ouray agency headquarters.