Mt. Clifton most likely got its name from its imposing position overlooking Mill Creek. It was founded sometime in the middle of the 19th century by George Hammon and his sons. They built and operated a store, flour mill, saw mill, and blacksmith shop in the area.

Soon after the Hammon's arrival the Howard's Lick Turnpike, the major road from Mt. Jackson to Orkney Springs and West Virginia, opened. A toll house was constructed in Mt. Clifton and the community became a rest stop for the many visitors traveling to resorts in Orkney Springs or West Virginia.

Like in other small communities in the area, commercial, social, educational, and spiritual institutions emerged. These include:

-The Mt. Clifton Methodist Church, constructed in 1884.
-The Mt. Clifton Store, constructed around 1900.
-The Mt. Clifton School, the first of which opened in 1852.
-The Mt. Clifton Odd-Fellows, organized in the early 19th century.
-The Mt. Clifton Mill, which first began operating in 1813.
-The Mt. Clifton Post Office, which opened in 1850 and was located in the local store.

Today the community's commercial interests have long since closed. Mt. Clifton Post Office was discontinued in 1900. The mill and school closed in the mid-1940s. A few decades later the final store also closed.

Only the church remains in operation and most of the structures that once surrounded it are abandoned or demolished.