In 1989, Archbishop Francesco Colasuonno, Apostolic Nuncio, took the initiative to expand the Roman Catholic Academy of Theology, which had been separated from the former Pázmány Péter University, into a new university with a Christian spirit. In May 1990, Dr. Péter Erdő, Dr. Mária Kopp, Dr. Tamás Roska and Árpád Skrabski established the Organizing Committee of the Catholic University Foundation. As a result of their one and a half year long struggle, the foundation of the university was supported by the Government of the Republic of Hungary, which made the buildings and plot of the former Perczel Mór barracks in Piliscsaba available for this purpose. On 30 January 1992, the Hungarian Catholic Bishops' Conference (HCPC) appointed Dr. Ferenc Gál as Rector and under his leadership re-established the first faculty of the University, the Faculty of Theology, and founded the Faculty of Humanities and Social Sciences. The latter institution has been forced to relocate several times in the past twenty years.
The postgraduate Canon Law Institute has been in operation since 30 November 1996 as a faculty, the Faculty of Law and Political Sciences since 3 April 1995 and the Faculty of Information Technology and Bionics since 24 June 1998. The Vitéz János Faculty (the legal successor to the Vitéz János Teacher Training College in Esztergom) was established in 2008 to provide teacher training for kindergarten and primary school, and has been merged into the Faculty of Humanities and Social Sciences on 1 July 2013 under the name of the Vitéz János Teacher Training Centre. On 25 March 1999, the University became a Pontifical University by Resolution N.1151/98 of the Congregation for Catholic Education, and was one of the fifty-two universities with a Pontifical Charter among the eight hundred Catholic higher education institutions worldwide. The Grand Chancellor of the University is the respective president of the HCBC; since 2015, Bishop dr. András Veres. The Rector of the University since 2019 is dr. Géza Kuminetz.