Through the direct intervention of Pope Clement VIII and with the co-operation of the Grand Master of the Order of St. John, then Cardinal Verdalle, as well as with the financial assistance of Bishop Tomaso Gargallo and the Maltese Diocese, the Jesuits founded the Collegium Melitense at Valletta, on the 12th November 1592.

In 1595 Grand Master Garsez laid the foundation-stone of the college premises and the adjoining Jesuits Church. 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 17th Century, Philosophy and Scholastic Theology formed already the core of higher studies within the same college.

On the 17th June 1672, Grand Master Antoine Manoel de Vilhena ratified the right of the Faculty to confer academic degrees in Philosophy and in Theology which had then been given to the Rector of the Collegium Melitense by the Father General of the Society of Jesus. The power of conferring academic degrees of Master of Philosophy and Doctor of Divinity had been granted to the Society of Jesus by Pope Paul IV in 1561 and reconfirmed by Pope Gregory XII by Apostolic Letters dated 9th May 1578. The General of the Society was, thereby, fully authorized to grant the same power to Rectors of those Jesuit Colleges which had attained the required standards. The Collegium Melitense had been carrying its educational and academic activities for more than 130 years.

In 1768, Grand Master Emanuel Pinto de Fonseca, following the example set by other European governments, expelled the Society of Jesus from the Maltese Islands. Papal authority intervened and allowed the Order of St. John to administer, on certain conditions, the property which belonged to the Jesuits. On the 22nd November 1769, Grand Master Pinto, through a Magisterial decree, raised the Collegium to the status of a Public University.

The Faculty of Theology, which formed the original nucleus of the University of Malta (from 1938 onwards designated as The Royal University of Malta by an Act of King George VI), remained ever since the senior Faculty, until by the Education Act, of 1978 it ceased to function as part of the University. By a degree and signed by H.E. Cardinal G. Garrone, Prefect of the Sacred Congregation for Catholic Education (dated 21st September 1978), the Faculty was authorized to function as an autonomous institution and grant academic degrees in Theology, Philosophy and Human Sciences.

The Faculty was incorporated in the University in virtue of an agreement signed by the Government and the Holy See on the 25 th September 1988.