University of Zagreb is the oldest not only in Croatia but also in South-Eastern Europe. The date of its official founded 23 September 1669, when the Roman Emperor and Hungarian-Croatian king Leopold I issued a law that recognizes the privileges and status of University educational institutions of the former Jesuit Academy, which operated on the territory of the free Royal city of Zagreb, the former capital of the Kingdom of Croatia and Slavonia. This date is the early history of the University of Zagreb in its struggle for the implementation of the rights received and getting worthy of a place among the respected and prestigious universities and academies in Central Europe.

The history of the University of Zagreb in its modern form begins with initiatives gykovskogo Bishop and a prominent Croatian benefactor Josip Juraj Strossmayer, when he in 1861 proposed to organize in the University's four faculties: medical, theological, philosophical and legal. The proposal was considered for several years, and in 1874, the Croatian Parliament adopted the initiative and issued a decree "About the University". In the same year, the University changed its name and became known as the Modern University of Zagreb.

Since 1990-ies, the University had received greater autonomy, at the same time began the accession to the Bologna process.