A customs office has operated at or near this crossing since 1865, initially by the Colony of British Columbia to inspect vessels arriving via the Columbia River, and after 1871 by the federal government of British Canada, additionally to inspect trains with the completion of the Nelson and Fort Sheppard Railway (N&FS) in 1893.

After correcting survey errors that placed some lots south of the border, the development was relaunched as Fort Sheppard in 1893.

The separate towns of Waneta and Fort Sheppard, north and south of the railway bridge across the mouth of the Pend-d'Oreille River, merged into the former after a few years, and Boundary City appeared on the US side.

If a First Nations link was more local, the meanings attributed to the name have included shape-shifter, rushing waters, burned area, and rolling waves.

A November 1892 newspaper reference called the place Juanita, a diminutive of Juana, a female Spanish name.