The Department of Transportation serves an umbrella organization for four subsidiary agencies which are directly responsible for different areas of the state's infrastructure.

The agency is tasked with operating the West Virginia Turnpike, an 88-mile (142 km) tolled stretch of Interstate 77 from Charleston to Princeton.

The authority also owns the West Virginia Central Railroad, consisting of 132 miles (212 km) near Elkins.

The West Virginia Central is operated by a private company, the Durbin and Greenbrier Valley Railroad.

Other State Rail Authority duties include promoting tourist and short-line railroads, operating three MARC train stations in the Eastern Panhandle, and helping to preserve or railbank lines targeted for abandonment.