With the help of the American Home Mission Society of the Congregational Church, the church was built to serve the several families who used the town of Sunol as their summer resort. In 1890, the church's Ladies Aid society (also known as the "glenside Helpers") was organized. In 1903 they helped furnish the church with gas lighting The church parsonage, which now serves as our office, Sunday school, and bride's room, was added in 1907-the same year that the Congregational Church in Mission San Jose donated their "old" pews to the church. In 1916 attendance dropped sharply and the church fell into what was called "the dark ages." The church appeared in several silent feature films during this period.

With renewed interest in 1949, the little church grew from four to more than 30 members, and was again poised to serve the community. In 1954 the church was painted brown and renamed "The Little Brown Church of Sunol" after the popular song of the time, "The Little Brown Church in the Vale."

Major renovation of the Sanctuary interior was completed in 1998, and the exterior of the church was renovated/repainted in April 2000.