After Nebraska Territory was organized in 1854, Dr. W. H. Goode came to establish Methodist missions. In 1855 Goode appointed Rev. William D. Gage to lead the Nebraska City Mission.
Construction of a church began at this site in 1855. It was dedicated in November 1856. Part of the original structure forms the south end of the current sanctuary. In 1861 the Nebraska Methodist Conference was organized at Nebraska City. In 1936 the conference designated this church as "Mother Church of Methodism in Nebraska."