In 1857 Father Joseph Biemans opened a parish school in a rented store building on Gay Street but was forced to close in 1861 due to the rigors imposed by the Civil War. Father Abram Ryan reopened the parish school in 1865. By 1874 the school, located on the eastern edge of Immaculate Conceptions Property and built by Father Francis Marron, contained multiple classrooms and space for a convent. The two story porch on the rear of the building was replaced by classroom additions in 1903.
Saint Mary’s School was originally staffed by lay school masters who were replaced by the Sisters of Saint Joseph in 1875. In 1887 the Sisters of Saint Joseph were replaced by the Sisters of Charity. In 1896 the Sisters of Charity were replaced by the Sisters of Mercy who staffed it until it was closed in 1969.