The gradual secularisation of Hungarian society from the 19th century onwards meant that the ecclesiastical university founded in 1635 by Cardinal Péter Pázmány, Primate of Nagyszombat, which was taken over by the state (royal) administration in the 1770s, could not be run in its entirety in a Catholic spirit. Therefore, the idea of creating a Catholic university by detaching the Faculty of Theology or by founding a new one independently of it was raised over and over again. In the course of the 19th century, Catholic universities were established in several countries of Western Europe and in America for the same reason. These institutions are not to be confused with the universities founded in the Middle Ages in countries that were committed to Christianity, even at state and social level. It was precisely the breakdown of the medieval unity of religion, state and society that made this new type of university necessary. However, attempts to establish Catholic universities in Hungary remained unsuccessful until the last decade of the 20th century. The ultimate reason for this was, on the one hand, that the Kingdom of Hungary and the Catholic Church were never completely legally separated. On the other hand, between 1948 and 1989, official ideology did not allow the development of a new Catholic higher education.
In 1989, the state proposed the reattachment of the Pázmány Péter Roman Catholic Theological Academy to Eötvös Loránd University. However, in Hungary, the separation of the Faculty of Theology from the state university was different from that in neighbouring Czechoslovakia. In 1950, Decree No. 23/1950 of the Presidential Council of the Hungarian People's Republic stipulated that the theological faculties should be separated from the universities and transferred to the competent churches. Thus, the Hungarian Catholic Bishop's Conference reorganised the Faculty of Theology, which had been separated from the university, under the name of the Roman Catholic Central Academy of Theology. The state recognised this institution as an academy of public law and granted it the possibility of awarding academic degrees in its own legal system. Since the Faculty of Theology in Budapest was still a purely ecclesiastical institution in 1989, the State could not unilaterally merge it with a public university. This would have required the consent of the Holy See, as it was a faculty of theology. This was never granted, however, as diplomatic relations between the Republic of Hungary and the Holy See were only re-established at the beginning of 1990 (9 February). The process that led to the establishment of Pázmány Péter Catholic University in its present form was initiated only following this.