West Virginia Baptists follow the same basic patterns of beliefs that have distinguished Baptists historically: the Bible as the sole authority for rule and practice; the belief in baptism by immersion for believers; the complete autonomy of each local congregation; the priesthood of every believer; the separation of church and state; and religious liberty.

The first Baptist church in present West Virginia was the Mill Creek Baptist Church in the Eastern Panhandle. Though it dissolved within a few years of its founding in the mid-1740s, it was a training station for several ministers who made their way over the mountains to do lasting work in Western Virginia. John Corbly and John, James, and Isaac Sutton were part of the Mill Creek Church and founders of the first two active Baptist churches west of the mountains, both of which continue to the present. Corbly and the Sutton brothers moved west, in part, because colonial Virginia's established church refused to license them to preach as Baptists.

Corbly settled in the Morgantown area about 1770 and gathered a congregation around him called the Forks-of-Cheat Baptist Church. His family was attacked by Indians on their way to church in May 1782. His wife and three of his children were killed in that attack, and two other children were scalped but lived. John Sutton helped form the Simpson Creek Baptist Church in Harrison County in about 1770. Baptist work in southern West Virginia began with the efforts of John Alderson Jr. in 1781.

By 1800, there were approximately 16 churches with 450 members within the boundaries of present West Virginia. Among the churches were 12 Particular Baptist (predestinarian), two General Baptist, one Seventh Day Baptist, and one Six Principle Baptist. Distances and rugged terrain dictated that for fellowship, mutual support, counseling of churches and ministers, and discipline of congregations, associations of churches in geographical proximity were needed. The first was the Greenbrier Association in 1800. By 1835, there were four associations with slightly more than 1,000 church members. By the time of the Civil War in 1861, there were six associations with almost 7,000 members.

The issue of slavery caused a division among Baptists nationally and in Western Virginia. In 1845, the Southern Baptist Convention was organized, and shortly thereafter Baptists primarily in the North organized themselves as the American Baptist Missionary Union. The Civil War brought a sharp decline in church membership and activity. Baptist churches were not only divided in loyalty, but numerous church buildings were damaged or destroyed, used as barracks for soldiers, for the storage of supplies, for prisons, and even as stables for horses.

By the end of the war, about two-thirds of West Virginia Baptist churches were aligned with the American (or Northern) Baptists and the remainder with the Southern Baptist Convention. The Baptist General Association of West Virginia, now known as the West Virginia Baptist Convention, was formed after the war in 1865. By 1869, the split between the Northern and Southern Baptists in the state was mended, and both Northern and Southern Baptists had united as the West Virginia Baptist Convention.

Baptist growth, like the general population of the new state of West Virginia, increased steadily following the war; there were approximately 250 churches in 1866 and 600 churches by 1900. After a slight drop in churches and membership during the Great Depression, Baptist growth reached its greatest numbers during the early 1950s—more than 800 churches.

By 2000, the West Virginia Baptist Convention, part of the American Baptist Churches in the USA, had a reported 463 churches and 108,087 adherents. Southern Baptists had 165 churches with a reported 43,606 adherents. Seventh Day Baptists have been influential in northern West Virginia where, for many years, they were closely related to Salem College. The Black National Baptists have churches primarily in the southern counties, and Independent Baptists are found throughout the state.

West Virginia Baptists have had an emphasis on evangelism and missions throughout their history, along with an involvement in social concerns such as the prohibition of alcohol. Baptists were particularly involved with rural ministries, including a railroad chapel car ministry to mining and lumber camps in the early 1900s. Numerous churches were organized as a result of itinerant mission work. Special attention to foreign immigrants in the coalfields was also emphasized at the turn of the century. Baptists have been leaders in the field of Christian education through local churches and schools, the most notable Baptist institutions of higher education being Alderson-Broaddus College in Philippi and Salem College (now Salem International University) in Salem.

West Virginia Baptists have served the state and the nation in many capacities. Notable are Robert C. Byrd and Jennings Randolph, who have served in the U.S. Senate with distinction. Baptists who have served as governors of West Virginia include Howard Mason Gore and Clarence Watson Meadows.

In 1940, a West Virginia Baptist Historical Society was formed at the West Virginia Baptist Convention's annual meeting, and in 1981 the society occupied a vault and an adjoining room of the West Virginia Baptist Conference Center at Ripley.