The school began as part of a Catholic mission in 1871 to serve and minister to newly freed slaves.

The money for construction of the school ($7,500) was donated by Katherine Drexel (1858–1955), founder and superior of the Sisters of the Blessed Sacrament, an order of nuns formed "to serve Indians and Colored People."

During 1964, Martin Luther King Jr. used the rectory as a meeting place to plan marches.

The events which occurred in St. Augustine, of which Martin Luther King Jr. played a key role, were an important catalyst in the passage of the Civil Rights Act.

The roof was removed during 2006 as part of a restoration project which has been stalled for an alleged lack of funding.