On December 31, 1791, some of the citizens of Troy gathered at Ashley’s Tavern to formally organize the Presbyterian Church of Troy. Over the next 200 years, the church would plant and nurture twelve more Presbyterian congregations. One of the new churches was the Second Presbyterian Church, whose cornerstone was laid at the corner of Sixth and Grand Streets in 1826.

In 1792, the Reverend Jonas Coe, from the Presbytery of New York, became the pastor of the Presbyterian churches in Troy and Lansingburgh. He was ordained in the first church meeting house, built near the southeast corner of Congress and First Streets. In order to “pay the bills” pews were sold by deed to members of the church. This method of conducting the “stewardship campaign” remained in effect until the 20th century.

After the death of Dr. Jonas Coe in 1822, Dr. Nathan Beman was called to the First Presbyterian Church. His pastorate was a strong one marked by the formation of several new Presbyterian churches as well as the struggle over the sin of slavery that consumed the entire nation.

Presbyterianism continued to grow in Troy, and a new building for the First Church was built at the corner of First and Congress Streets in 1836. That building is now owned by Russell Sage College.

On May 10, 1862 the Great Troy Fire destroyed the Second Presbyterian Church as well as 700 other buildings in Troy. Though such devastation brought great mourning, nine days after the fire, an appointed committee chose the west end of Fifth Avenue between Grand and Fulton Streets to build their new church. First United Presbyterian Church stands there today.

By the turn of the century, growth in Presbyterian witness began to fade and church attendance was at an all time low, including in the Troy churches. However Second Presbyterian Church flourished with the strong pastorates of Dr. Paul Hickok, Dr. Frederick W. Evans, and the Rev. George Borthwick. In 1955, Second Presbyterian merged with Ninth Presbyterian, which was located at Fifth Avenue and Jay Street and was pastored by the Rev. Charles Rice, to form the Fifth Avenue Presbyterian Church. The Rev. Borthwick served the merged church until 1977.

In 1947, the First Presbyterian Church called the Rev. Dr. S. Edward Young, who served as its pastor for 23 years. The Rev. David Blackshear was called to First Church in 1970. The congregations of the First and Fifth Avenue churches became First United Presbyterian in 1971. The Rev. Borthwick and the Rev. Blackshear served as co-pastors. 

After the Rev. Borthwick’s retirement and the Rev. Blackshear’s
departure, the Reverends John Merrill and Charles Rice served as interim pastors. In 1978, Dr. Milton Gardiner was called as pastor.  The Rev. Jane Brawley served as Associate Pastor from 1983 to 1984, the Rev. Elizabeth Hall, from 1985 to 1992. The Rev. Gardiner retired in 1989.

In 1990, the Reverends Barbara Anderson and Mark Smutny, a clergy-couple, were called as co-pastors. In 1998 they moved to Pasadena, California. They were followed by interim pastors Dr. R. Peter Durkee and the Rev. Lois Ann Wolff. The Rev. Alexandra S. Lusak served as Pastor and Head of Staff from August 2000 until October 2010. Interim Pastor Jacquelyn Pinkowski served from November 2010 until October 2011. Interim Pastor Rick Otty served from October 2011 until April 2014.

First United welcomed it's new Pastor and Head of Staff, the Reverend Gusti Linnea Newquist in May of 2014.