In April 1788, Col. George Clendenin was ordered to proceed west from present Lewisburg to construct a military outpost near the confluence of the Kanawha and Elk rivers as a defense against the Indians. He arrived with a band of 30 rangers and established the first permanent settlement within the present boundaries of Charleston. A fort, named Clendenin's Fort or Fort Lee, in honor of Gen. Richard Henry "Light Horse Harry" Lee, was built on land Clendenin had purchased from Judge Cuthbert Bullitt of Prince William County, Virginia.

The site, at the present corner of Brooks Street and Kanawha Boulevard near downtown Charleston, offered a good spot for a canoe landing and a vantage point above the river. Completed in May 1788, the fort structure was about 36 feet long and 18 feet wide, with a height of about 18 feet. A stockade, constructed of logs placed upright and set side by side in ditches, was about 250 by 175 feet.

The establishment of Fort Lee gave some protection to the settlers, but the threat of Indian attack remained until 1794. A story grew through the years that the fort was besieged by Indians in 1790 and that a woman heroine, "Mad Anne" Bailey, brought ammunition to the fort from Lewisburg. No basis of fact could be found for this incident, however.

The Clendenins, George and his brothers, William and Alexander, sold the fort to Joseph Ruffner in 1796, and it subsequently fell into disrepair. The stockade lasted until 1815, and the blockhouse was used as a dwelling place for many years. John P. Hale purchased the original lot and blockhouse in 1872 and moved the building, which finally burned down in 1891. Wood from the blockhouse was used to make a table now on display in the West Virginia State Museum.

The first child of European descent born in Charleston, Lewis Ruffner, entered the world at the fort on October 1, 1797. A monument was erected in 1915 at the site, which marks the site of Charleston's beginnings.