The church today known as the Church of the Covenant began as a mission Sunday school in a space above a stable on East 40th Street. It was initiated by a group of young professional members of the Church of the Covenant on 35th Street and Park Avenue, which had opened in 1865. The group was headed by J. Cleveland Cady, a young New York architect who became perhaps best known for the original Metropolitan Opera House (1891) and the Museum of Natural History (1890). Cleveland Dodge provided a major portion of the funding. To accommodate the rapidly growing congregation of the mission, Cady designed a country chapel with an adjourning Parish House, which opened in 1871 at 310 East 42nd Street. The mission was called Memorial Chapel to celebrate the reunion of the Presbyterian Church after the civil war.
In 1893, the (original) Church of the Covenant merged with the Brick Presbyterian Church, then located at Fifth Avenue and 37th Street. The 42nd Street property was also transferred to Brick, who retained ownership until the 1960’s. In 1893 the mission became an organized, independent congregation and assumed the name Church of the Covenant.
The original Parish House was replaced in 1927 with half-timbered Elizabethan style, designed to blend with the neighboring Tudor City, a residential complex built in the late 1920s. In 1950, 42nd Street was lowered by several feet, necessitating the addition of a granite and limestone base below the entry level of the building, the repositioning of the entry doors and the addition of a new flight of steps leading up to these doors.