West Virginia's institutions were controlled by 25 boards with 129 members when a 1909 joint legislative committee recommended eliminating the boards and consolidating management and fiscal controls under one agency. The 1909 West Virginia legislature created the Board of Control, a state agency, "with full power to manage, direct, and control" certain state institutions.

Initially, the Board of Control took over the state mental health institutions, the three miners' hospitals, penal institutions, and Schools for the Deaf and Blind at Romney. The board's scope was expanded greatly in 1911, when it was given responsibility to manage the state tuberculosis sanitarium at Terra Alta and the West Virginia Colored Orphans Home at Huntington. At the same time it was given control of the financial and business affairs of West Virginia University and 12 other state colleges and educational agencies. A number of city institutions, such as the Kings Daughters Hospital and City Hospital in Martinsburg, were included in the board's fiscal oversight responsibilities. By the early 1930s, 59 agencies of one type or another had been placed under the Board of Control.

As state government continued to grow, more specialized oversight agencies were created. In 1933, a state director of purchases was appointed and took over that responsibility from the Board of Control. In 1947, the business affairs for West Virginia University and the state colleges were transferred to the WVU Board of Governors and the State Board of Education, respectively. By the early 1950s, the Board of Control's responsibility had dwindled once more to care of the state mental health and penal institutions. A 1957 reorganization of state government transferred these remaining institutions to the new Department of Mental Health and to the Commissioner of Public Institutions. The Board of Control ceased to exist on June 30, 1957.