The Saint Thomas Choir School was founded in 1919 at the request of Dr. T. Tertius Noble, organist and choirmaster of Saint Thomas Church Fifth Avenue. Dr. Noble had previously been the organist and choirmaster at York Minster in England, where all of his boy singers were students at their choir school.

When the rector and vestry of Saint Thomas called Dr. Noble to New York in 1913, Dr. Noble accepted the position with the understanding that a Choir School would be necessary to achieve the musical standard desired for the parish. A new school opened in 1919 on 55th Street with 21 boys.

The school remained at that site, with periodic renovations and additions, until 1987, when it relocated to its current location, a purpose-built fifteen-story building on 58th Street that houses the choristers and full-time faculty. In 1996, the school expanded to include third grade. It now nurtures and educates approximately 30 boys in grades three through eight.