Short-line railroads were built to serve communities or industries not reached by major railroad companies. Their locomotives, trains, and people were very much a part of the places they served and retained a personal, often idiosyncratic, character that made them more like neighbors than corporations.

To cut construction and equipment costs some short lines were built as narrow gauge, usually three feet between the rails. The railroad south of Clarksburg to Glenville was narrow gauge, as was the line from Grafton to Belington. Both were acquired by the Baltimore & Ohio Railroad and converted to standard gauge in the 1890s. The West Virginia Midland served the lumber industry and the resort hotel at Webster Springs until the hotel burned; the line closed in 1930—31. The Valley River Railroad narrow track served a sawmill at Mill Creek, and carried the public to Valley Head until 1931. Most unusual was the Twin Mountain & Potomac, built 27 miles south from Keyser to serve the extensive peach orchards. Its six-year life ended in 1919. The state's last narrow gauge, the Mann's Creek Railroad, carried coal from Clifftop to coke ovens in the nearby New River Gorge until 1956.

Standard-gauge lines had the great advantage of being able to interchange cars with the main line railroads, meaning that goods did not have to be unloaded and reloaded. The Lewisburg & Ronceverte brought rail service to Lewisburg in 1907. It was converted to electric operation, but soon succumbed. There were many lines built to serve coal mines, such as Campbells Creek, Winifrede (still in operation under a different name), Kellys Creek, and Kellys Creek & Northwestern, all along the Kanawha River east of Charleston. Each was less than 25 miles long, but several had four locomotives to handle the heavy traffic. The Chesapeake & Ohio absorbed several coal railroads south of Thurmond, and others near the lumber town of Rainelle.

The Middle Creek, Buffalo Creek & Gauley, and Middle Fork railroads all connected to the Coal & Coke (later B&O) line between Charleston and Elkins. The last two were also associated with lumber companies. The Morgantown & Kingwood worked large mines with 48 miles of track and a dozen locomotives, becoming part of the B&O in 1922. Neighboring West Virginia Northern remained independent, beginning as a coal hauler in 1899 and finally quitting (as a tourist line) in 1999. The Preston Railroad, on the Maryland line, was independent until abandoned in 1960. The Dry Fork was built to carry lumber from the mill at Horton 31 miles to a Western Maryland Railroad connection, and survived until 1936.

Nearly all the state's short lines are gone, but the State Rail Authority owns two, the South Branch Valley (once B&O) south from Romney, and the West Virginia Central (formerly B&O and Western Maryland) serving Elkins. Both have tourist trains as well as freight service. The Durbin & Greenbrier Valley also runs on state-owned track, south from Durbin.