[1] The Catholic Faculty of Theology has its roots in philosophical-theological studies started by Bishop Stephen II of Zagreb in the early 13th century.

His successor Augustin Kažotić established the Zagreb Cathedral School in the early 14th century, and is thus considered the founder of higher education in Croatia.

[2]: 34–35 The Jesuit College (Gymnasium Capitale) in Gradec, Zagreb, was granted a right to give academic titles by a charter of King Leopold on 23 September 1669.

[2]: 35 After the abolishment of the Jesuit Order in 1773, Queen Maria Theresa promoted the Pauline general studies on 5 August 1776 to the Royal Academy of Sciences, which was constituted of faculties of theology, law, and humanities.

The University of Zagreb was officially opened on 19 October 1874, and its first rector was a Catholic priest and a professor of history and canon law Matija Mesić.