The museum collections are diverse and include a flag collection from the Confederate States Army;[9] a set of early medical tools from West Virginia's pioneering physician Joseph Robins;[10][6] and examples of Homer Laughlin China Company (now known as the Fiesta Tableware Company) Fiesta Tableware, a Newell-based ceramics manufacturer.

[12] In 1940, the state purchased the Wilson Stone and sent it to the University of Michigan archeologist Emerson F. Greenman, who concluded that it was, in all likelihood, a fraud.

[12][13][14] The earliest history of the museum started with the West Virginia Historical and Antiquarian Society in 1890, as an established exhibit in the state capitol.

[18][19] In summer 2009, a newly renovated museum building debuted, after being closed for five years for a US $17.9 million dollar remodel.

[15][20] In 2011, the United Mine Workers of America (UMWA) labor union's president Cecil Roberts wrote a detailed letter of complaint about issues of inaccurate depictions of their organization in the museum, as well as issues of inaccurate history, particularly around the Battle of Blair Mountain a violent labor dispute.