The Collegium Melitense, the predecessor of the University of Malta, was founded on 12 November 1592 by the Order of the Society of Jesus at Valletta.  The foundation became a reality through the direct intervention of Pope Clement VIII; the indispensable co-operation of Cardinal Hugh Loubenx de Verdalle, Grand Master of the Order of Saint John; and the financial assistance of Tommaso Gargallo, Bishop of Malta and Gozo.

The building of the premises of the Collegium Melitense and the adjoining Church of Jesus was started in 1595.  The foundation stone was laid by Grand Master Martin Garzes.  Teaching in Grammar and the Humanities, however, had already began in 1593, while lectures in Moral Casuistry began to be delivered towards 1599.  Throughout the seventeenth century, Philosophy and Scholastic Theology already formed the core of higher studies within the same Collegium.

On the 7th June 1727, Grand Master Antoine Manoel de Vilhena authorized the Faculty of the Collegium to confer academic degrees in Philosophy and Theology a faculty given to the Collegium by the Minister General of the Society of Jesus.  The Society of Jesus had been granted the right to confer the academic degrees of Master of Philosophy and Doctor of Divinity by Pope Paul IV in 1561, a faculty reconfirmed by Pope Gregory XIII through Apostolic Letters dated 9th May 1578.  The Minister General of the Society was thereby, fully authorized to communicate the same faculty to rectors of Jesuit Colleges whenever these institutions had attained the required academic standards of higher education.  The Collegium had already by then  carried on its educational and academic activities for one hundred and thirty years.

In 1768, Grand Master Emmanuel Pinto de Fonseca, on the example of other European governments and not without the pressure, expelled the Society of Jesus from Malta,  Papal authority intervened to keep the Collegium functioning and, for this reason and on several conditions, authorized the Order of St. John to administer the property that belonged to the Jesuits.  Through a Magisterial decree of 22nd November 1769, Grand Master Pinto, raised the College to the status of a Public University.

The Faculty of Theology, that formed the original nucleus of the Collegium became the senior Faculty of the University of Malta, designated The Royal University of Malta by an Act of King George VI in 1938.  It remained its senior Faculty for over two hundred years, that is until 1978, when by the Education Act of 1978, ceased to function as part of the old university but continued its academic activity as an autonomous institution.  This was officially announced by His Grace Mgr. Giuseppe Mercieca, Archbishop of Malta, and new Chancellor of the Faculty, on 15 September 1978.  This was later confirmed by a decree of Gabriel Marie Cardinal Garrone, Prefect of the Sacred Congregation for Catholic Education, dated 21 September 1978.  The decree authorized the Faculty of Theology to continue its activity as an autonomous institution and declared that its academic degrees will continue to receive recognition.  It continued to grant degrees in Theology, Philosophy and Human Sciences.  The official inauguration of the Academic year took place on 14 October 1978, at the Mater Admirabilis College, Tal-Virtu, Rabat that had been designated as its new seat.

During the first academic year of its new status, the Faculty of Theology proceeded with the courses already in progress, namely those leading to the Diploma in Sacred Theology (S.Th.Dip.), Baccalaureate in Sacred Theology (B.S.Th.), and Mastership in Sacred Theology (M.S.Th.). Later on through a decree of the Sacred Congregation of Catholic Education dated 19 May 1980, the Faculty of Theology was authorized by the Holy See to set up an Institute of Religious Studies and to offer courses in Philosophy, Theology, and Social Teaching of the Church leading to the Degree of Bachelor of Arts in Religious Studies (B.A. in Rel. St.). The Institute started functioning in October 1980.

The Faculty of Theology was re-incorporated in the University of Malta by an agreement signed by the Government of Malta, and the Holy See on 25 September 1988.