After several rebuilds, the fort was ultimately abandoned in 1854, after it had become part of United States territory following settlement in 1846 of the northern boundary dispute.

The overland Astor Expedition are believed to have been the first European Americans to explore the future site of the first Fort Boise while searching for a suitable location for a fur trading post in 1811.

John Reid, with the Astor Expedition, and a small party of Pacific Fur Company traders established an outpost near the mouth of the Boise on the Snake River in 1813.

[4] Donald Mackenzie, formerly with the Astor Expedition and representing the North West Company, established a post in 1819 at the same site.

In the fall of 1834, Thomas McKay, a veteran leader of the annual Hudson's Bay Company (HBC) Snake Country brigades,[5] built Fort Boise, selecting the same location as Reid and Mackenzie.

In July 1834, Thomas McKay's Snake Country brigade was trapping far to the east and met the party sent by Wyeth to select a site and build Fort Hall.

[6] Although Fort Boise may technically have been built as a private venture of Thomas McKay, it was fully backed and supported by McLoughlin and the HBC.

[13] In 1866, the Oregon Steam and Navigation Company constructed and launched the Shoshone, a sternwheeler, at the old Fort Boise location.

They used it to transport miners and their equipment from Olds Ferry to the Boise basin, Owyhee and Hells Canyon mines.

They built a mule-driven sawmill on Cottonwood Creek, got a lime kiln underway, and opened a sandstone quarry at the small mesa known as Table Rock.

The National Guard occupied it until 1919, when the Public Health Service obtained it for a center for veterans of World War I and tuberculosis patients.

During rehab efforts following the Foothills Fire in 1997, firefighters found several unexploded 75 mm (2.95 in) artillery shells and other ordnance.

The final "wild west show" scene of the Clint Eastwood movie Bronco Billy was filmed in Fort Boise Park in October 1979.