Although certain academies (notably of philosophy and theology) were established as Jesuit higher education in what is now Slovenia as early as the seventeenth century, the first university was founded in 1810 under the Écoles centrales of the French imperial administration of the Illyrian provinces.

That university was disbanded in 1813, when Austria regained territorial control and reestablished the Imperial Royal Lyceum of Ljubljana as a higher-education institution.

They gained momentum in the fin de siècle era, when a considerable number of renowned Slovene academians worked throughout Central Europe, while ever more numerous Slovenian students were enrolled in foreign-language universities of the Austro-Hungarian Empire, particularly in the Austrian and Czech lands.

In the 1890s, a unified board for the establishment of a Slovenian university was founded, with Ivan Hribar, Henrik Tuma, and Aleš Ušeničnik as its main leaders.

In 1898, the Carniolan regional parliament established a scholarship[clarification needed] for all students who were planning a habilitation under the condition that they would accept a post at Ljubljana University when founded.

Together with Danilo Majaron, Rostohar convinced the central government of the Kingdom of Serbs, Croats and Slovenes in Belgrade to pass a bill formally establishing the university.

The seat of the university was in the central Congress Square of Ljubljana in a building that had served as the State Mansion of Carniola from 1902 to 1918.

The building was first designed in 1902 by Jan Vladimír Hráský, and was later remodelled by a Czech architect from Vienna, Josip Hudetz.

After the invasion of Yugoslavia in April 1941, the university continued to function under the Italian and Nazi German occupation, despite numerous problems and interference in its autonomous operation.

Following the end of the Second World War, the first and only foreigner elected to hold the office of chancellor was the Czech professor Alois Král, who had lectured at Faculty of Technical Sciences since 1920 and also held the position of dean thereof four times.