Beginning and development of higher education and educational institutions in Mostar and Herzegovina date from the end of the 19th century. Roots of higher education in Mostar are related to establishment of the Franciscan Theological School that launched its activity in 1985. That was the first school at the university level. The Teacher Training School began its work after the Second World War (1950). It was followed by the Higher Engineering School (1959), Higher Agricultural School (1960), departments of the Faculty of Law and Faculty of Economics, which became autonomous faculties in 1976. From 1977 to 1992 both higher schools and faculties worked as a part of the University “Džemal Bijedić” in Mostar and the official language was Croatian-Serbian or Serbian-Croatian language. Both the name and the official language were changed after 1992. Since then, the name is the University of Mostar and Croatian was introduced as official language instead of a former Croatian-Serbian.

During the Homeland War, on April 7, 1992, the teaching process was interrupted because the first grenades fell on the Student House and the Faculty of Economics. The University ceased with its work only in the period from April to July 1992 due to the ongoing aggressor bombing of Mostar. Summer exams were held in Široki Brijeg for students who did not reside in Mostar. The following two academic years (1992/93 and 1993/94) the lectures for the first year of study were organized in Neum and Široki Brijeg. Since the academic year 1994/95, the lessons have been held in partially renovated university facilities in Mostar. 

After recovering from the consequences of the war, the University commenced strong development, and thus Mostar became a university city.