Head of the Catholic Faculty of Theology is the Great Chancellor and the Management of the Faculty.

The office of the Great Chancellor of the Faculty is regularly held by the diocesan bishop of the Archdiocese of Zagreb or, if the seat is hindered or vacant, the person who is substituting the diocesan bishop of the Archdiocese of Zagreb. The Great Chancellor represents the Holy See at the University, at the Faculty itself, and also represents the Faculty at the Holy See. His duty is to make sure that the original Christian thought and life is preserved and advanced at the Faculty and that the community with the universal and local Church is maintained.