The history of the University began on September 23, 1669, when the Holy Roman Emperor Leopold I issued a decree granting the establishment of the Jesuit Academy of the Royal Free City of Zagreb.

The beginnings of the later university date back to 23 September 1669 when Emperor and King Leopold I Habsburg issued a decree granting the establishment of the Jesuit Academy of the Royal Free City of Zagreb.

[6] According to that document the study of philosophy in Zagreb acquired a formal and legal status as Neoacademia Zagrabiensis and officially became a public institution of higher education.

In 1776 Empress and Queen Maria Theresa issued a decree founding the Royal Academy of Science (Latin: Regia Scientiarum Academia).

During the Austro-Turkish War of 1788–1791 and following the Austrian occupation of Belgrade on 8 October 1789 the Royal Academy requested to be granted the university status with the following argumentation: If we consider the current circumstances in which serious consideration is given not only to the removal of obstacles to science, but also to the appointment of our local citizens to all services in these kingdoms, and if we also consider for a moment future opportunities, not only that the part of Croatia that is still sobbing under the Turkish yoke but also the kingdoms of Bosnia and Serbia – [...] – will be liberated and that these glorious kingdoms will be almost expanded.

We believe that it is not only proud and useful, but also absolutely necessary to have in our environment such a university in which – when all obstacles to scientific work are removed and when funds for its development are obtained – number of local youth will be educated in all the sciences and noble skills for performing various services in their homeland.

Bishop Josip Juraj Strossmayer in 1861 proposed to the Croatian Parliament the founding of a university at Zagreb.

[10] In 1898, the Academy of Forestry (Šumarska akademija) was founded as part of the Faculty of Philosophy, which encompassed all technical studies.

Also in 1919 the School of Veterinary Medicine (Veterinarska visoka škola) was founded; it transformed into a university faculty in 1925.

[15] With a decision of 7 October 1992, the Ministry of Science and Technology entered FFDI into the register as a Scientific Research Organization in philosophy and it became a part of the Croatian Studies Department of the University of Zagreb.

[17] FFRZ has a formal relationship with Laudato TV to "work together to promote and implement educational, cultural and scientific activities in the Christian and humanistic atmosphere".

[18] In 2017 there were two current research studies at the Faculty of Philosophy and Religious Sciences: On 5 May 2017 a symposium was held on "Religions and Migration: Displaced Persons and Refugees".

His deputy is Dalibor Renić, Provincial Superior of the Croatian Province of the Society of Jesus based in Zagreb.