In 1850, Bishop Martin J. Spalding delegated Father Francis Chambige to establish a home for dependent boys; the Sisters of Charity did the same for girls. Two sisters were assigned to the farm in order to take care of the boys until 1857, when the Brothers of the Sacred Heart took over. The first orphans to arrive lived in the seminary, but when it became too crowded, the seminary gave some farmland for an orphanage and vegetable garden. During the Civil War, soldiers from both the North and the South swept through and took the food from the orphanage.
St. Thomas Orphanage provided a home and education for more than ten thousand boys over its history. The home remained in operation at St. Thomas until 1889 when it was closed following a devastating fire. The orphanage relocated to the city of Bardstown and then moved to Louisville, merging with St. Vincent orphanage for girls. St.Thomas-St. Vincent orphanage continued operation until 1984.