By the time West Virginia was established in 1863, the Methodist Church claimed the largest number of congregations in the new state. Challenged only by the Baptists, Methodism had been successful in meeting the needs of people scattered in sparsely populated settlements throughout the mountains.

Several reasons account for the success of Methodism in West Virginia. First, the organizational structure of the church allowed a small number of people to create a "class" led by a local lay leader. These classes were linked by ordained clergymen who visited regularly to lead worship services and to administer the sacraments. The geographical area over which these clergymen rode was called a circuit, and the clergymen were called circuit riders. The classes in a circuit were bound together in a quarterly conference, and several circuits were grouped together into an annual conference. Conferences met for worship and instruction, and the annual conference assigned pastors to the circuits.

The second reason for the success of Methodism was the inspiring commitment of the leadership of the early church and their circuit riders. Bishop Francis Asbury, the best-known early American Methodist, visited West Virginia more than 30 times. Bishop Asbury's enthusiasm and dedication were replicated by circuit riders Robert Ayres, Asa Shinn, Henry Bascom, Thomas Ware, John Smith, and many others who rode circuits in West Virginia in the late 18th and early 19th centuries.

The third reason for the success of Methodism was the democratic theology of its message. Unlike the Congregational and Presbyterian denominations, in which salvation was reserved for a few, the message of Methodism was that salvation was attainable by all. While the organization of Methodism was authoritarian, the theology of founder John Wesley and his followers treated all people as equals—a popular view in frontier America.

Two Methodist circuits were established in the area of West Virginia in the 1780s. The Redstone Circuit included southwestern Pennsylvania and northern West Virginia. It was eventually subdivided into the Ohio Circuit to the north and the Clarksburg Circuit to the south, the latter located primarily in West Virginia. The second was the Greenbrier Circuit in southeastern West Virginia. Perhaps the earliest class on the Greenbrier Circuit was formed a few miles from Union, Monroe County, in 1780. By 1786, the class had erected Rehoboth Church, claimed to be the first church built west of the Allegheny Mountains. Bishop Asbury visited Rehoboth several times, holding sessions of the Greenbrier Conference there in 1792, 1793, and 1796. From here Methodism continued to move west into the Kanawha Valley, where the Little Kanawha Circuit was formed in 1799.

The early part of the 19th century saw a tremendous increase in religious zeal, sparked in part by the Second Great Awakening. Methodism participated extensively in this movement, and as congregations grew they encountered differences that eventually led to schisms, two of which were felt keenly in West Virginia. The Methodist Protestant Church (1830) grew out of differences over the authority of the bishop and the role of the laity. The Methodist Episcopal Church, South (1844), a more divisive rift, was created primarily by differences over slavery. A "Plan of Separation" was drafted in an effort to seek an amicable dissolution, but this was a failure from the outset and intense competition erupted to claim congregations for the Northern Methodists or the Southern Methodists. West Virginia was a major battleground in this struggle, and Northern Methodist clergy were a major force in the movement for statehood.

Before the century ended, controversy over the holiness movement and creationism led to further division. The Church of the Nazarene, the Pilgrim Holiness movement, and several other denominations or movements resulted from these controversies. Each established congregations in West Virginia, further fragmenting the Methodist movement.

But Methodism was not all discord. Congregations in the three branches of Methodism ministered effectively to their communities, contributed to missionary outreach, and established or participated in church-sponsored education. The Northern Methodists established West Virginia Wesleyan College, and the Southern Methodists established Morris Harvey College (now the University of Charleston).

During the early 20th century, all three branches of Methodism became more structured and more urbanized. Members of the clergy were increasingly better educated, and the church assumed a more aggressive social mission. While this growth often created tension between the church leadership and the rank-and-file, membership grew rapidly throughout the state. Unlike the previous century, the 20th century became one of reconciliation and reunification. After more than 25 years of negotiations, the three major branches of Methodism—the Methodist Episcopal Church; the Methodist Episcopal Church, South; and the Methodist Protestant Church—merged in 1939 into a single Methodist Church.

In 1968, the Methodist Church merged with the Evangelical United Brethren Church, itself the result of a merger of the United Brethren in Christ (UB) and the Evangelical Association (EV) in 1946, to create the United Methodist Church. The UB and EV denominations had developed primarily among the German speaking populations of Pennsylvania, Maryland, and Virginia. The UB church was a significant force in West Virginia from the 1820s, but the Evangelical Association had only a handful of congregations in the state.

Today United Methodism is faced with interesting challenges. The episcopal and educational leaders of the denomination move toward a vision of a global church, but many local congregations, particularly in small towns and rural areas, remain wary of such views. Membership, while increasing in other countries, is now declining in the United States and West Virginia. In 2023, there were 904 United Methodist churches in West Virginia, a decline from 125,336 members in 1,341 churches at the beginning of the 21st century.