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The university's roots reach back to 1859 when a theological seminary was established with the encouragement of Maribor bishop and patriot Anton Martin Slomšek. More faculties were established during the late 1950s and early 1960s; the faculties of economics, business, and technology in 1959, agronomy and law in 1960, and pedagogy in 1961. The university's opening ceremony occurred on 19 September 1975. The 1970s was a decade of exponential rise in the number of higher education institutions in the former Yugoslavia when alongside Maribor universities in Osijek, Rijeka, Split, Mostar, Podgorica, Bitola, Banja Luka, Kragujevac and Tuzla all opened their doors.

Rectors of the University of Maribor were Dali Džonlagić, Alojz Križman, Ludvik Toplak, Ivan Rozman and Igor Tičar. In late 2017 and early 2018, Jan Žan Oplotnik was acting rector for almost one year. In 2018 Zdravko Kačič was elected rector.