After the decline of late medieval universities in the Kingdom of Hungary, a Jesuit University was established in 1635. Since the kingdom’s heartland was under Ottoman occupation, it started to operate in Nagyszombat (now Trnava, Slovakia). In 1667 the two original faculties, Humanities and Theology, were supplemented by a faculty of law. In 1769 a decree by Maria Theresa placed the university under state supervision and added a medical faculty. In 1777 it was moved to the Castle of Buda, then, in 1784, to Pest. The solemn opening of 1780 saw a student enrolment of c.400. The 1777 Ratio Educationis added new departments (among others, agriculture, physics and mechanics, architecture, geography, and aesthetics), and, in 1782 and 1784 respectively, departments for engineering and veterinary medicine were set up. Alongside the university, higher education also included vocational/technical academies; the most prestigious of these was the Academy of Mining in Selmecbánya (now Banská Stiavnica), founded in 1763, which, from 1807, also had a chair in forestry. In 1797 Count György Festetics established an agricultural academy on his estate in Keszthely.

Following Decree 16 of 1791, which ordered the teaching of Hungarian in gymnasiums, academies, and at the University, in 1792 a chair of Hungarian was established. It served as an inter-faculty department offering a non-compulsory one-year course. Since the language of education was Latin (apart from the period between 1784 and 1790, when it was German), the name of the course was Institutiones Linguae et Litteraturae Hungaricae. From 1812 the course was offered under the title Lingua et Litteratura Hungarica, and from 1817 it was divided into two complementary courses, Litteratura Hungarica and Lingua Hungarica.

Though attracting only a handful of students, the Hungarian department quickly gained scholarly and political weight amid the linguistic debates of the era. The early incumbents were András Vályi (1792–1801), Miklós Révai (1802–1807), and Ferenc Czinke (1808–1830). To various degrees, all of them participated in the political and linguistic discussions about the vernacular. In his 1810 Beszéd a magyar nyelv ügyében (“Address on the issue of the Hungarian language”), Czinke defended Latin as language of state administration. In his inaugural lecture, Révai famously asserted that “We cannot speak Hungarian” (or, in the oration’s Latin: “Nescimus hungaricae”). What Révai meant was not that only half of the kingdom’s population spoke Hungarian, but that even those whose mother tongue was Hungarian had an imperfect command of it. Accordingly, Révai considered his main task to uphold an ideal grammatical system and distribute it through university education. He used the position to prepare his 2-volume grammar (Elaboratior Grammaticae Hungaricae, 1806).

A Hungarian department that offered more than a language course was established in 1837 in the faculty of humanities (which, in turn, only served as preparatory to law and theology). Its chair was István Horvát, head librarian of the National Library from 1815 and the professor of diplomatics from 1823. Although a disciple of Révai, Horvát was less interested in the systematics of an ideal Hungarian than its ancient history. He maniacally searched through historical documents from biblical times and antiquity to the Middle Ages to uncover hidden traces of Hungarian vocabulary permeating every human language. While his outdated ideas and methods were increasingly subjected to mockery and ridicule, Horvát’s charisma and nationalist zeal exercised considerable influence on his students, including the novelist József Eötvös and the poet Mihály Vörösmarty.

A Diet decree replaced Latin with Hungarian in state administration and legislation in 1844. However, philosophy, history, physics, and mathematics continued to be taught in Latin until 1849. Non-Hungarian language departments were established only reluctantly: petitions for a Slovak chair were turned down in 1838 and 1846. A Slavic department was founded in the 1850s, a Romanian one in 1861.

In the course of these developments, the university gradually moved from serving a (non-ethnic, class-based) hungarus identity towards promoting a national culture. Many prominent members of the non-Hungarian national movements of the early 19th century were graduates from, or affiliated with, the university. The dwindling of the aesthetics department, which had been founded as early as 1774 on humanist Bildung principles (chaired between 1792 and 1842 by Lajos [Ludwig] Schedius), exemplifies the national compartmentalization of literary culture in the mid-19th century.

The post-Ausgleich era was marked by a proliferation of the university system. New institutions were established, mainly in Budapest: the Royal Joseph University of Engineering in 1872, the Academy of Music (with Liszt as president and Ferenc Erkel as director) in 1875, the Ludovika Academy of Military Science in 1872, the College of Fine Arts in 1908. The first university of arts and sciences outside the capital, the University of Kolozsvár (present-day Cluj, Romania) was set up in 1872. The József Eötvös Collegium (named after the late minister of culture), founded in 1895, was modelled after the French École Normale Supérieure and provided accommodation for talented students from the provinces.