The current Saint Thomas Church is actually the fourth church for the parish. The third church, which was also at the current site at Fifth Avenue and Fifty-third Street, suffered a devastating fire in 1905. The first worship service in the current church was on October 4, 1913.

Designed by the distinguished architectural firm of Cram, Goodhue and Ferguson and completed in 1913, Saint Thomas Church is built in the French High Gothic style, with stone ornamentation of the later Flamboyant period in the windows, small arches of the triforium, and stonework surrounding the statuary in the reredos. The flat wall behind the altar is characteristic of English cathedrals, and the magnificent reredos, one of the largest in the world, is strongly suggestive of the single, massive windows that terminate the naves of many English churches designed in the Perpendicular style.

Saint Thomas is of cathedral proportions, with the nave vault rising 95 feet above the floor. The church is built completely of stone, according to medieval construction principles, using load-bearing rib vaulting without the space-spanning benefits of steel. The size, spacing, and number of columns and arches are precisely what is necessary to support the structure – and give it the unique acoustical properties associated with churches built of the same materials and in the same way during the Middle Ages.