The beginnings of theological studies in Slovenia are connected with the Christianising of the Slovene nation and the Carolingian Renaissance. They took on a more definite form in the 11th and 12th centuries with the establishment of the monastic schools which were linked with significant European centres. In accordance with the decrees of the Council of Trent, a theological school was opened in 1589 in Gornji grad where 16 theologians received education under the leadership of six priests; this marked the beginning of public higher education. In 1619 the Jesuits introduced lectures in casuistry (moral theology) at their college in Ljubljana which involved public disputation on theological theses. From 1708 printed theses for Slovene school disputations and defences were preserved. By the decrees of the Council of Trent, theological schools within monasteries were established by the Cistercians, Carthusians, Conventual Franciscans, Franciscans and Capuchins. After the dissolution of the Jesuit order in 1773, the theological studies were transferred to the seminary. 

Under Josephinism 1783 -1791 the monastic schools and diocesan houses of studies were suppressed; the seminarians were educated in the "general seminary" in Graz.When the French established the Illyrian Provinces (1809-1813), they introduced Central schools in Ljubljana which became the Academy - University in 1811 with the right of conferring degrees. Within the University, the Faculty of Theology organised a four-year undergraduate programme. The first Rector of the University was Jožef Balant, who later became the Archbishop of Gorizia. After the departure of the French, the Austrian government restored theological studies at the Lycee. In 1851 under the Ordinary of Ljubljana, Bishop A.A.Wolf, the management of study was taken over by the diocese. 

In 1859 Bishop Anton Martin Slomšek transferred the episcopal seat from St. Andraž (Carinthia) to Maribor (Styria) and opened the Slovene Theological College. In 1898, the first Slovene theological journal Voditelj v bogoslovnih vedah (A Guide to Theological Disciplines) was published there. The college functioned regularly until World War II.

In 1919, the University of Ljubljana was re-established and comprised five faculties: theology, law, philosophy, technology, and medicine. The Faculty of Theology (TEOF) was housed in the former students’ hostel Alojzijevišče. After 1949 it no longer operated as part of the University. The Faculty of Theology was excluded from the University by the government on June 31, 1952. In the Autumn of 1972, an extension was built to Alojzijevišče where the lectures are now delivered. In 1968 the Maribor Unit of the Faculty of Theology was opened for the three final years of study. After 1993 it gradually extended to a complete theological course. In May, 1991 the Faculty regained its status as a state institution and on November, 18, 1992 it was reintegrated into the University of Ljubljana. In the academic year 1993/94 a two-subject study programme was introduced: in Ljubljana in connection with the Faculty of Arts and in Maribor with the Faculty of Education. Since 1997 the lectures in Maribor have been delivered in the new diocesan building Andreanum. Since 1921, with a several year interruption after World War II, the Faculty of Theology has published a journal Bogoslovni vestnik (Theological Quarterly).