On Sunday, October 12, 1823, a new Protestant Episcopal congregation was organized in a meeting room at 44 Broome Street. In July 1824, in accordance with the resolutions of that congregation, the cornerstone for the new St. Thomas Church was laid at the intersection of Broadway and Houston Street. By 1866 this part of town had turned seedy, impelling the worshippers to build a new church, which endures, at 53rd Street and Fifth Avenue.
Saint Thomas's current structure, finished in 1914 and the fourth church built for the congregation, was designed in the French High Gothic Revival style by Bertram Grosvenor Goodhue and Ralph Adams Cram.