Presbyterians have been active in New Albany since its beginnings in 1813. The Scribner family, which founded the town, brought their Presbyterian faith with them from New England. Presbyterians in New Albany and the neighboring town of Jeffersonville, Indiana, formed a joint congregation in 1816 under the direction of Reverend James McGready. By December 1817, the congregation had split. The New Albany contingent subsequently established the First Presbyterian Church of New Albany. The first formal meeting of the church took place at the Scribner’s house on East Main Street. The location of church meetings varied until the congregation built a permanent structure in 1854. The building stood on the east side of Bank Street between Main and Market streets. It served First Presbyterian until the congregation consolidated with St. John United Presbyterian Church in 1969.

Conflict over abolition split the First Presbyterian congregation in 1837. Most members viewed slavery as wrong but wished to remain passive observers. Others urged active participation in abolitionism. The later group formed the Second Presbyterian Church of New Albany, which soon became a center of antislavery activity. According to local tradition, the congregation used their new building, now known as the Town Clock Church, to shelter runaway slaves. Church leaders such as Reverends Sneed and Atterbury, and congregation elders like James Brooks, the church hid and transported runaway slaves well into the Civil War.

In 1853 the Presbyterian Church split due to pressures from the large size of the congregation. The split formed the Third Presbyterian Church. All three Presbyterian Churches functioned separately for over 60 years. In 1917, the Second and Third churches united as the Hutchinson Presbyterian Church. The new congregation named itself after a prominent pastor.

In 1969, New Albany Presbyterians united as one congregation. They formed the present day St. John United Presbyterian Church. The congregation is located in a former building of Second Presbyterian Church.