Presbyterian Scotch-Irish settlers were among the first Europeans to settle in present-day West Virginia, arriving in the early 1700s. They started churches across the region, especially in the Eastern Panhandle and Greenbrier Valley. Early leaders such as Daniel McGill, John McCue, and John McElhenney helped grow the faith by starting churches and opening schools like the Lewisburg Academy.

Henry Ruffner, an important Presbyterian leader, opposed slavery on economic grounds and supported public education, helping shape schools in both Virginia and West Virginia. The Civil War caused a split in the church between Northern and Southern Presbyterians.

In the late 1800s and early 1900s, Presbyterians expanded into coal-mining areas. After World War II, the church grew quickly, especially around Charleston. Women played a big role through leadership, education, and missions.