West Virginia's first capital, Wheeling, was the largest city in the new state and the site of the statehood movement resulting from Virginia's secession from the Union. The First and Second Wheeling Conventions, the creation of the Reorganized Government of Virginia, and the action of the latter to allow the creation of a new state all took place in Wheeling. When the new state came into being on June 20, 1863, its first meeting was in Wheeling's Linsly Institute. That day, Governor Arthur I. Boreman asked the legislature to choose a permanent seat of government. The legislature declined and authorized the governor to acquire the Linsly Institute building to serve as a temporary capitol.

By 1869, Wheeling's critics noted that it was a temporary location and was not centrally located. A movement to relocate the capital "where it will develop the natural resources of the State the most, and accommodate the largest number of inhabitants," resulted in legislation, passed February 26, 1869, to move the seat of government to Charleston.

The State House Company constructed a state capitol building in Charleston, which was occupied in December 1870. Legislators from around the state complained that Charleston was not a suitable location for the capital, declaring that the city lacked adequate transportation, hotels, and restaurants. Discontent with Charleston, and Wheeling's promise of a new capitol building, resulted in legislation on February 20, 1875, to temporarily move the capital back to Wheeling. Fearing the loss of income, Charleston residents secured an injunction against the removal of state records. The case made its way to the Supreme Court of Appeals, which eventually dissolved the injunction and allowed the move.

The debate over a permanent location for the capital continued, and it was decided to put a choice of three cities before the voters. In the election on August 7, 1877, Charleston received the most votes (41,243), followed by Clarksburg (29,942) and Martinsburg (8,046). An examination of the county-by-county election results indicates that the voters chose the cities closest to them, tending to discount politics as a major factor in the decision.

In 1878, Charleston's previous state house building and lot were donated to the West Virginia Board of Public Works by the State House Company, the city of Charleston, and the Kanawha County Court, the latter two of which had pledged to retire an outstanding debt on the property. State government occupied a new building in 1885, though it was not completely finished until 1887. Governor Emanuel W. Wilson hosted a ball and banquet to formally open the new capitol on January 5, 1887. That capitol burned on January 3, 1921, as did a subsequent temporary “pasteboard capitol” in 1927. Meanwhile, state government offices, leaders, and the legislature had already moved into the current capitol on Charleston’s East End, even before its completion; it was officially dedicated on June 20, 1932.