Fort Nez Perce, later Fort Walla Walla, was established in 1818 by the North West Company near the junction of the Walla Walla and Columbia Rivers. In 1821 the Hudson’s Bay Company took over as the area continued to be claimed by Great Britain. In 1846 the boundary dispute between the U.S. and Britain was resolved and the location was found to be part of the United States due to the Oregon Treaty. However, the treaty did allow Hudson's Bay Company navigation rights on the Columbia River to supply their fur posts, and clear titles to their trading post properties allowing them to be sold later if they wanted. HBC continued to operate the Fort Nez Perces for another decade until it was abandoned at the outbreak of war with the Yakima Indians and finally burned in 1857.

The first military Fort Walla Walla was a temporary fort built in 1856 on the south side of Mill Creek, directly west of Kibler and 5 miles northeast of the growing community of Walla Walla. Col. Edward J. Steptoe supervised the building, which consisted of a blockhouse and stockade. The early name for this fort was "Fort Steptoe".

The second military Fort Walla Walla was built in October and November of 1856, on the north side of Mill Creek, 6 miles east of the junction of the Walla Walla River with Mill Creek. The compound went from the present Main Street south to the current First Avenue to about Palouse Street. This fort included barracks, stables, officer's quarters and sheds.

The third Fort Walla Walla was built the following spring in 1857 on 13th Avenue and Rose Street, adjoining the city of Walla Walla. This fort was more extensive than the previous two forts and covered 613 acres. The original buildings were made of adobe brick which were later boarded over and painted white. Along with the officers quarters and troop barracks, the fort included parade grounds, stables, a blacksmith's shop, granary, storehouse, sheds, and a saw mill. Fifteen of these "fort-era" buildings exist today.

Fort Walla Walla was formally deactivated in 1889 and abandoned in 1911. Today it is the site of the present day Fort Walla Walla park, cemetery and museum complex, as well as the Veterans Hospital and grounds.