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.

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.

The university has entered the top 1% of institutions in physics and, of the nine institutions entering the top 1% in this field, the University of Maribor did so with the highest number of citations, according to an analysis of data from Essential Science Indicators from Thomson Reuters.The University of Maribor has cooperated in European Framework Programmes since 1998 and the number of international research projects is increasing each year.