The Army called it Rattlesnake Camp at first, an unofficial supply drop along the creek of the same name in what is now Harney County. As wagon trains increased through eastern Oregon and miners flooded the backcountry, the demand for military protection grew. Rattlesnake Creek sat near the geographic center of eastern Oregon, an ideal location for a headquarters. On August 16, 1867, the Army established a permanent outpost near the creek's mouth. They named it Camp Steele, but Major General Henry W. Halleck, commander of the Military Department of the Pacific, had other ideas. He suggested honoring Brigadier General William S. Harney, who had commanded the Department of Oregon in 1858 and 1859. By September 14, 1867, the post was officially Camp Harney.

General Crook's campaign against the Northern Paiute from 1867 to 1868 deployed an unlikely force. Companies from the 1st and 8th Cavalry Regiments, mounted infantry from the 9th and 23rd Infantry Regiments, and Indian scouts from the Wasco and Warm Springs tribes, peoples who had fought the Paiute for generations. Camp Harney resupplied these columns as they pursued bands across eastern Oregon and into northern California in the conflict known as the Snake War. The campaign succeeded. In 1869, Crook and Wewawewa signed a treaty at Fort Harney ending the raids. The Paiutes agreed to settle on a reservation north of Malheur Lake. Camp Harney sat within those boundaries, Army soldiers assigned to keep white trespassers out and Paiutes in.

By 1877, Camp Harney had grown into a proper frontier town. A large parade ground ran north to south, flanked by a headquarters building and guardhouses. The commanding officer had his own home, five additional officers' quarters stood nearby, two of logs, three of frame construction. Three log barracks housed enlisted men, four more log buildings sheltered soldiers with families. To feed this population, the camp maintained mess halls, kitchens, a bakery, and a slaughterhouse. Quartermaster's storehouses and a military commissary supplied everything from ammunition to flour. A hospital treated the sick and injured. A sawmill cut timber from the pine stands north of the camp. A blacksmith shop and stables for 150 horses kept the cavalry mobile. Four civilian clerks, two masons, a saddlemaker, shoemaker, painter, baker, and four laundry maids completed the community.

The Paiutes kept the peace. The settlers did not. Despite the Army's presence, ranchers grazed cattle on reservation land throughout the 1870s. This unchecked encroachment helped spark the Bannock War of 1878. Newspapers reported Camp Harney in imminent danger of being overrun. They exaggerated, but the camp did return to its wartime role as supply depot and military headquarters, positioned at the center of the conflict zone. General Oliver O. Howard defeated the Bannocks and Paiutes within months. The prisoners that followed, those 543 souls held through the winter of 1878-79, would be scattered to reservations across the West. The fort lingered until 1880, then closed. The high desert slowly reclaimed its buildings. Today, only gravestones mark where Fort Harney once stood.