Fort Thornburgh was first established in September 1881 by Captain Hamilton S. Hawkins near the present site of Ouray, Utah. In April 1882 the fort was moved under the direction of Captain J. P. Schindel, acting in Captain Hawkins's temporary absence. The new location of the fort at the mouth of Ashley Creek continued until its abandonment in 1884. This short-lived fort is more famous for the events that brought its name and its establishment than for its scant three years of existence.

The history of Fort Thornburgh begins with hostilities on the White River Ute Reservation in Colorado, in 1879. Nathan Meeker came as agent to the Ute band following the troubled departure of Edward H. Danforth in 1878. Meeker believed he could transform the Ute warriors into sedentary agriculturalists, and pay off several debts at the same time. He provoked a confrontation in September 1879 when he ordered fifty acres of pasture land plowed. The enraged Indian custodian of the land dragged Meeker from his office and publicly beat him. Meeker immediately telegraphed Washington and asked that federal troops be dispatched to the reservation. Major Thomas T. Thornburgh was ordered out of Fort Steele, Wyoming, to assist the frightened agent.

Thornburgh and nearly 200 men left Fort Steele on 21 September 1879. The Utes attacked the troop as they entered the reservation boundaries on 29 September 1879, killing Major Thornburgh and several other men. The column was held under siege until help arrived from Fort Steele six days later. Meanwhile, the White River Agency was attacked on 30 September 1879. Meeker and several of his assistants were killed, and Meeker's wife and daughter were captured along with another woman and two children. The women and children were later released unharmed, but the outrage caused by the attack brought into flame an already smoldering fire.

Governor Frederick W. Pitkin used this attack to call for the removal of all Indians from Colorado, including the Umcompahgre Utes who had helped obtain the release of the captives. Governor Pitkin had the support of mining and cattle interests who had been eyeing the vast Ute holdings in western Colorado. Removal was proposed to either Indian Territory (Oklahoma) or to the existing Ute reservation in the Uinta Basin. The Mormon-United States conflict over polygamy left little clout for Utah Territory in Washington, and so the Colorado Utes were moved into Utah. The White River band was placed on the existing Uintah Ute Reservation and the Umcompahgre Utes were placed on the new Ouray Reservation to the south and east.

The Secretary of War decided to construct a fort in the Uinta Basin to hold the Utes on the reservation and to quiet any potential hostilities between the Indians and whites. Major Hawkins was ordered south out of Fort Steele at the head of four companies of the 6th Infantry on 21 August 1881. They established Fort Thornburgh on 17 September. The Secretary of the Interior complained to the Secretary of War that the troops would provide a bad influence for the Utes, and that the fort had commandeered most of the good agricultural land on the Ouray Reservation. The fort was moved in the spring of 1882 to the mouth of Ashley Creek, 6.5 miles northwest of present-day Vernal, Utah.

The Secretary of War planned an elaborate $84,000 fort consisting of thirty-two brick or frame buildings to house Hamilton's four companies of men. During the summer of 1882 the men began work on eight temporary adobe buildings and laid out the boundaries for the fort, which encompassed 21,851 acres. These structures were to serve until Congressional appropriation could be obtained. The men also began work on the Carter Road, built as a supply road through the Uinta Mountains to connect Fort Thornburgh with the nearest Union Pacific railhead--Carter, Wyoming. The main force left Fort Thornburgh and returned to Fort Douglas on 16 October 1882, leaving a detachment of thirty men commanded by Lieutenant Lyman W. V. Kennon to act as guard detail and continue construction on the fort.

Three companies returned to Thornburgh on 23 June 1883 under the command of Major Edward G. Bush. Congress appropriated a disappointing $1,500 toward construction in 1883, far below the $84,000 requested by the Secretary of War. Bush abandoned the thought of improved quarters and spent the summer of 1883 working on Carter Road between the fort and the government sawmill in the Uintas. The troops returned to Fort Douglas on 3 October, leaving only a caretaker to look after the fort. Thornburgh was officially abandoned sometime during the winter of 1883 or spring of 1884.

Several reasons were given for the abandonment of the fort. First, a portion of the acreage had already been claimed by settlers, and the government had never obtained clear title to the land. More important was the conviction that there would be no difficulty from the Utes during the winter months, and that any summer trouble could be quickly quelled by dispatching troops from Fort Douglas or Fort Bridger, especially now that the Carter Road had been completed.

The decision to abandon Fort Thornburgh proved unsound when inter-band warfare broke out among the Utes during the winter of 1885-86. The departments of the Interior and of War both sent investigators to the Uinta Basin, and recommended the establishment of a permanent fort. General George Crook selected the new Fort Duchesne site in August 1886; it was three miles above the junction of the Uintah and Duchesne rivers and midway between the Whiterocks agency and the Ouray agency headquarters. Squatters took over the abandoned site, and ten years later, in 1894, were given title to the property. A portion of Fort Thornburgh now lies within the boundary of Maeser, Utah.