When the first Rutgers congregation dedicated its first sanctuary on the corner of Henry and Rutgers Streets in Lower Manhattan on May 13, 1798, that congregation and sanctuary were the third unit of the Collegiate Presbyterian Church of New York City. It was built on a plot of ground donated by Colonel Henry Rutgers (who also donated land for the university in New Jersey that is named for him), and paid for by contributions from the members. 

By 1830, Rutgers had become the largest Presbyterian church in the denomination, with 1,157 members. The old frame church was replaced in 1843 with a large stone structure (still standing and in use as the Roman Catholic Church of St. Teresa of Avila). The congregation decided in 1863 to move “uptown,” taking over the Lenox Chapel at 29th and Madison, where a small, pastorless Presbyterian congregation was in residence. That group eventually became members of Rutgers. Although the membership was now less than half of its all-time high (many additional Presbyterian churches having been opened in the city), the congregation, in 1873, demolished the Lenox Chapel and built an elaborate church on the spot.

Population changes and the post-Civil War prosperity which transformed the church neighborhood into a largely business district eroded the membership to a low level. In 1887 the congregation accepted the invitation of the Presbytery’s Church Extension Committee to move to a new section of the city at 73rd and Broadway. Through proceeds from the sale of the Madison Avenue property, a chapel was built in 1888 and a large church on the corner was dedicated in 1890.

At the new location and under new leadership, the church flourished, as the Upper West Side underwent a building boom. In 1925 the present aggregation of sanctuary, church house and office building was erected. By 1942, the congregation welcomed a merger with the Harlem/New York Church.

The years of World War II and its aftermath brought significant changes to the Upper West Side. A core of Rutgers congregants remained loyal, but their residences became widely scattered in the city and their numbers slowly declined. There followed a time of great change during which there were three installed pastors, three interim pastors, an unsuccessful merger with the West Park Church, a reconfiguration of the interior of the Church House, and a remodeling of the church sanctuary.

In September 2009, Rutgers called the Reverend Dr. Ondrej (Andrew) Stehlik as its 22nd Installed Pastor. Dr. Stehlik has made his mark in Rutgers history with his innovative approach to worship and progressive worldview.