The Pontifical Faculty of Theology and Civil de Lima has its origin in the historic decision of Master of the Order of Preachers, Brother Augustine recuperato of Favencia, to create the Province of San Juan Bautista, on 4 January 1540. This province would be held at the Convento de Santa María del Rosario de Lima. also teaches the creation of a "study" (college) to form readers Arts (philosophy) and theology.
The top of the new Province met in Cuzco on July 1, 1548. They decided to create and operate the "studio" in the city of Lima, with some students and professors. Nearly three years later, with developing theological studies, by Royal Charter of May 12, 1551, the King of Spain created the University of Lima, with all the privileges of the University of Salamanca. Theological studies were incorporated into the University, serving this as the basis for its existence. Thus, the Faculty of Theology was established, the first Faculty of the New University. St. Pius V also approved with the brief "Exponi Nobis" of July 26, 1571. In 1574, she took the name of University of San Marcos.