Fort Harney was used as a supply depot and administrative headquarters from 1867 to 1880 during the Army's campaign against Northern Paiute bands in Eastern Oregon and the Bannock uprising in the same area.

In 1864, the U.S. Army had begun using a site along Rattlesnake Creek, in what is now Harney County, Oregon, for temporary supply drops.

Rattlesnake Creek was located near the center of eastern Oregon, making it an ideal place for a military supply depot and administrative headquarters.

[6][7][8] The Indian raids in eastern Oregon ended in 1869 after a treaty was signed by General Crook and Wewawewa, the chief of the area's dominant Paiute band.

[11][12][13][14] During the Bannock War, Camp Harney once again served as an important Army supply depot and military headquarters.

[15][16] However, the US Army forces under General Oliver O. Howard quickly defeated the Bannocks and Paiutes engaged in the uprising.

[5] On 13 September 1982, the Malheur reservation lands were officially returned to the public domain except for the 320-acre (1.3 km2) Fort Harney site which was retained by the Army.

The fort structures were built on a flat west of Rattlesnake Creek between steep ridges that flanked the stream.

In addition to Army troops, the post had four civilian clerks, two masons, one saddlemaker, a shoemaker, a painter, a baker, and four laundry maids.