On October 12, 2004, the Croatian Bishops' Conference, on its 29th plenary session, held in Zadar, adopted a Decision on the Establishment of the Catholic University of Croatia.

Bishop Ivan Šaško, a professor at the Catholic Faculty of Theological of the University of Zagreb, was appointed interim rector.

[2] On July 3, 2008, the Ministry of Science, Education and Sports issued a license to the university to offer programs in psychology, sociology, and history and with equal conditions of employment for five years.

On that occasion, Bozanić explained the reasons for the establishment of the university: "The basis for the establishment of this University is a commitment of the Catholic Church to assist the Croatian system of higher education while carrying out its mission and to streamline its opportunities in the social space because the Church believes that it's very important, and for that there were no preconditions in the past decades.

In October 2015, the Ministry of Science, Education and Sports issued a license for research activities in the field of biomedicine and healthcare to the Catholic University of Croatia, and in November 2015 a licence for an undergraduate and graduate programme in nursing.

In October 2019, the Ministry of Science and Education granted the Catholic University of Croatia a licence to offer a two-subject undergraduate programme in history.

In September 2020, the Ministry of Science and Education issued a licence to the Catholic University of Croatia to offer a two-subject graduate programme in sociology.

In June 2020, the Ministry of Science and Education granted the Catholic University of Croatia a license to offer an integrated undergraduate and graduate programme in medicine.