In 1996, Congress designated an 11-county area in southern West Virginia as the National Coal Heritage Area. These counties were Boone, Cabell, Fayette, Logan, McDowell, Mercer, Mingo, Raleigh, Summers, Wayne, and Wyoming. The legislation authorized the National Park Service to enter into a cooperative agreement with the state of West Virginia to provide support for developing partnerships and conserving resources throughout the region. Congressman Nick J. Rahall, of West Virginia's Third District, led the effort to establish the heritage area.

The 1996 congressional vote implemented the Omnibus Parks and Public Lands Management Act. The act allowed the National Park Service to develop resource protection initiatives for areas of national importance through the use of partnerships and private ownership rather than the traditional methods of federally owned parklands.

For more than 80 years, southern West Virginia enjoyed economic growth and development based on coal mining. However, during the second half of the 20th century, coal industry employment declined and many southern counties suffered from unemployment and out-migration of people. The primary mission of the heritage area is to preserve, protect, and interpret lands, structures, and communities associated with West Virginia's coal mining heritage and to stimulate tourism and economic development.

The National Coal Heritage Area operated initially as a loose partnership of tourism and history agencies of West Virginia state government with the National Park Service, under the direction of a steering committee. In 2002, the West Virginia legislature established an independent National Coal Heritage Area Authority to manage the heritage area. With the addition of Lincoln County and the Paint Creek-Cabin Creek area of Kanawha County, the area now includes 13 counties.