In June of 1892 a Methodist Protestant congregation was organized in Logan Township, Hitchcock County, by the Rev. M.H. Noe. When the congregation outgrew its sod church, this stone structure was built on this site on land donated by Rebecca Hart. The stone was quarried five miles southwest of the church, and all work was done by hand, including cutting and hewing the rock to size. The church building was completed and dedicated in 1900 during the pastoral term of the Rev. J.E. Darby. The first board members were Wyman Mills, James L. Hoyt, Aaron McKnight, C.O. Hart, and Minnie Smith.
In 1904 the St. Paul Methodist Protestant Church was merged with the United Brethren in Christ and in February, 1907, the group was organized as United Brethren. A vigorous Sunday School program was inaugurated. The Stone Church also served as the center of community activity. Regular church services were discontinued in 1951.
In 1975 the Stone Church Community Association was formed to restore and preserve the structure as a memorial to area pioneers.