Although Boone County was named for the great American frontiersman, it was another explorer, John Peter Salley, who had a more significant impact on what was to become Boone County. In 1742, while on an exploring trip, Salley and companions discovered coal near the present day community of Peytona. The discovery of coal has played a vital role in fueling the steel mills and power plants of the United States, and remains the backbone of Boone County's economy. In pioneer days, a small log courthouse was constructed when the county seat was known as Ballardsville. That name source was St. Clair Ballard, a Virginia legislator. It was through his efforts that the county was named for Daniel Boone. Boone had rescued Ballard's mother from the Indians and reared her as his own child. Ballardsville was torched by Union soldiers during the Civil War but citizens rebuilt it near the old site. In 1865, a courthouse was constructed from brick. That structure was condemned in 1913, and the foundation of the present courthouse was begun a year later. The present courthouse, constructed of Indiana limestone, was completed in 1921. The exterior is very impressive and the edifice is on the National Register of Historic Places.

On June 20, 1863, when a new state was born out of the Civil War, Boone County Virginia, became Boone County, West Virginia.

In 1906, Madison was incorporated as the county seat. Madison derived its name from Colonel William Madison Peyton, who led the movement for the formation of Boone County. Peyton was instrumental in developing the Coal River Valley. There are three other municipalities in Boone County--Danville, Whitesville, and Sylvester.