The first Episcopal Church in what is now West Virginia was built about 1740 at Bunker Hill in Berkeley County. It is still in use today as an unorganized mission, where an annual service is conducted each September. Its successor is Zion Church in Charles Town.

Several other congregations began in the 1700s, and still others in the 1800s. In the Charleston area, St. John's Episcopal Church can trace its roots back to 1837, and parishioners there moved out to create All Saints Church in South Charleston and the Church of the Good Shepherd in Kanawha City. Trinity Episcopal Church in Huntington held its first services at the Cabell County Courthouse in Barboursville in 1869 but soon moved to Huntington. In the 20th century, its membership fanned out to create three other parishes in the region.

Like the state itself, the Episcopal Church split from Virginia. At the national convention in Boston on October 9, 1877, a resolution passed creating the new Diocese of West Virginia. The initial convention of the new diocese met at St. John's in Charleston, with 14 clergy and 16 lay delegates. Their first choice as bishop, the Reverend J. H. Eccleston of New Jersey, turned down the appointment. At a subsequent meeting, delegates took 11 ballots before they chose George William Peterkin, a native of Maryland. On May 30, 1878, he was consecrated a bishop at St. Matthew's Church, Wheeling, the largest in the new diocese with 220 communicants. Bishop Peterkin established the diocesan office in Parkersburg and built the Church of the Good Shepherd there in 1891.

The second bishop was the Reverend William Loyall Gravatt, who had been born in Virginia and was rector at Zion Church, Charles Town, when he was elected bishop coadjutor on July 26, 1899. When Bishop Peterkin died in 1916, Gravatt became bishop and moved the diocesan headquarters to Charleston. The third bishop, the Right Reverend Robert Edward Lee Strider, was a native West Virginian, born April 9, 1887, in Leetown, Jefferson County. He was rector at St. Matthew's, Wheeling, when he was consecrated bishop coadjutor there in 1923. He became bishop in 1939 and moved the diocesan office to Wheeling.

In 1944, a committee began searching for a church camp site to honor the first bishop and his wife. Diocesan trustees eventually purchased land from the Hampshire Club on the South Branch of the Potomac River near Romney. Today the Peterkin Camp and Conference Center honors all three of the first bishops with the main lodge named Gravatt Hall and the chapel named for Bishop Strider.

Sandscrest Farms near Oglebay Park at Wheeling came to the diocese in the early 1950s, through the will of Mr. and Mrs. Harry S. Sands, members of St. Luke's on the Island, Wheeling. Planned as a retirement home for Episcopalians, it is used instead as a retreat for small conferences, and the Diocesan Council conducts three of its four quarterly meetings there each year. Reynolds Memorial Hospital in Glen Dale was owned by the diocese until 1973, when it was given to the community. The first official Diocesan Center was established in October of 1964 when Helen Ruffner Ritz gave a house and land on Virginia Street in Charleston in memory of her late husband, Judge Harold A. Ritz. The diocesan office is now permanently located there.

Bishop Strider had announced in 1949 that he intended to retire April 9, 1955, on his 68th birthday. William Camrock Campbell became the fourth bishop of the diocese on May 10, 1955, with more than 2,500 people attending the services at the Charleston Municipal Auditorium. The fifth bishop was Robert Poland Atkinson, elected bishop coadjutor on February 17, 1973. He became bishop when Bishop Campbell retired January 1, 1976. He ordained the first women priests in 1977 and took semi-retirement in 1989, when Bishop John H. Smith was elected.

Bishop Smith came from Vermont. At the time of Bishop Smith's retirement in 1999, there were 78 parishes and mission churches in West Virginia. During his ten years, the emphasis was on cluster ministry, which combined smaller churches with a ministry team to avoid each parish paying the full cost of clergy. More than half of the congregations are now part of one of the 11 clusters established in the diocese, including two that include a church in a neighboring state and diocese. Michie Klusmeyer served as bishop from 2001 to 2022.

As of 2021, there were 6,405 baptized Episcopalians in West Virginia, more than a one-third decrease from the beginning of the century. The current Episcopal Bishop of the state is the Rt. Rev. Matthew D. Cowden.