The settlement of Clifton, Kansas was laid out in 1859 and named for the surveyor. In 1862, the fledgling community was deluged with threats of Indian attacks and in August 1862, Fort Clifton was built about three miles west of the original townsite. The fort was abandoned in the spring of 1863.
In 1870, the settlement of Clifton was moved to its present-day site in both Washington and Clay Counties. The exact location of Fort Clifton has since been lost but is thought to have been near Fort Brooks in Cloud County.