In 1893 the Anglo-Catholic Sisterhood of the Holy Nativity, affiliated with the Cowley Fathers (Society of St. John the Evangelist) began work in the parish and at the adjacent St. Timothy's Hospital.

The cornerstone for the church building was laid on July 18, 1862 by Bishop Alonzo Potter.

The church was consecrated by Bishop William Bacon Stevens on February 14, 1863, as one of his early official episcopal acts.

The studios of Victorian Anglo-Catholic stained glass artist Charles Eamer Kempe (1837-1907) designed the majority of the church's windows as memorials to members of the local Merrick and Cope families.

The stations of the cross are the work of Thorsten Sigstedt (1884-1963), a Swedish American woodcarver with studios in Bryn Athyn, Pennsylvania.