The area was called Boise long before the establishment of Fort Boise by the federal government. The original Fort Boise was 40 miles (64 km) west, near Parma, down the Boise River near its confluence with the Snake River at the Oregon border. This private sector defense was erected by the Hudson's Bay Company in the 1830s. It was abandoned in the 1850s, but massacres along the Oregon Trail prompted the U.S. Army to re-establish a fort in the area in 1863 during the U.S. Civil War.

The new location was selected because it was near the intersection of the Oregon Trail with a major road connecting the Boise Basin (Idaho City) and the Owyhee (Silver City) mining areas, both of which were booming. During the mid-1860s, Idaho City was the largest city in the Northwest, and as a staging area, Fort Boise grew rapidly; Boise was incorporated as a city 156 years ago in 1863. The first capital of the Idaho Territory was Lewiston in north central Idaho, which in 1863 was the largest community, exceeding the populations of Olympia and Seattle, Washington Territory and Portland, Oregon combined. The original territory was larger than Texas. But following the creation of Montana Territory, Boise was made the territorial capital of a much reduced Idaho in a controversial decision which overturned a district court ruling by a one-vote majority in the territorial supreme court along geographic lines in 1866.

Designed by Alfred B. Mullett, the U.S. Assay Office at 210 Main Street was built in 1871 and today is a National Historic Landmark.

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