Split into Czech and German universities
It soon became clear that neither the German-speaking Bohemians nor the Czechs were satisfied with the bilingual arrangement that the university had established after the revolutions of 1848. The Czechs also refused to support the idea of the reinstitution of the 1349 student nations, instead declaring their support for the idea of keeping the university together, but dividing it into separate colleges, one German and one Czech. This would allow both Germans and Czechs to retain the collective traditions of the university. German-speakers, however, quickly vetoed this proposal, preferring a pure German university: they proposed to split Charles-Ferdinand University into two separate institutions.
After long negotiations, Charles-Ferdinand was divided into German Charles-Ferdinand University (German: Deutsche Karl-Ferdinands-Universität) and Czech Charles-Ferdinand University (Czech: Česká universita Karlo-Ferdinandova) by an act of the Cisleithanian Imperial Council, which Emperor Franz Joseph sanctioned on 28 February 1882. Each section was entirely independent of the other, and enjoyed equal status. The two universities shared medical and scientific institutes, the old insignia, aula, library, and botanical garden, but common facilities were administered by the German University. The first rector of the Czech University became Václav Vladivoj Tomek.
In 1890, the Royal and Imperial Czech Charles-Ferdinand University had 112 teachers and 2,191 students and the Royal and Imperial German Charles-Ferdinand University had 146 teachers and 1,483 students. Both universities had three faculties; the Theological Faculty remained the common until 1891, when it was divided as well. In the winter semester of 1909–10 the German Charles-Ferdinand University had 1,778 students; these were divided into: 58 theological students, for both the secular priesthood and religious orders; 755 law students; 376 medical; 589 philosophical. Among the students were about 80 women. The professors were divided as follows: theology, 7 regular professors, 1 assistant professor, 1 docent; law, 12 regular professors, 2 assistant professors, 4 docents; medicine, 15 regular professors, 19 assistant, 30 docents; philosophy, 30 regular professors, 8 assistant, 19 docents, 7 lecturers. The Czech Charles-Ferdinand University in the winter semester of 1909–10 included 4,319 students; of these 131 were theological students belonging both to the secular and regular clergy; 1,962 law students; 687 medical; 1,539 philosophical; 256 students were women. The professors were divided as follows: theological faculty, 8 regular professors, 2 docents; law, 12 regular, 7 assistant professors, 12 docents; medicine, 16 regular professors, 22 assistant, 24 docents; philosophy, 29 regular, 16 assistant, 35 docents, 11 lecturers.
The high point of the German University was the era preceding the First World War, when it was home to world-renowned scientists such as physicist and philosopher Ernst Mach, Moritz Winternitz and Albert Einstein. In addition, the German-language students included prominent individuals such as future writers Max Brod, Franz Kafka, and Johannes Urzidil. The "Lese- und Redehalle der deutschen Studenten in Prag" ("Reading and Lecture Hall of the German students in Prague"), founded in 1848, was an important social and scientific centre. Their library contained in 1885 more than 23,519 books and offered 248 scientific journals, 19 daily newspapers, 49 periodicals and 34 papers of entertainment. Regular lectures were held to scientific and political themes.
Even before the Austro-Hungarian Empire was abolished in late 1918, to be succeeded by Czechoslovakia, Czech politicians demanded that the insignia of 1348 were exclusively to be kept by the Czech university. The Act No. 197/1919 Sb. z. a n. established the Protestant Theological Faculty, but not as a part of the Charles University. (That changed on 10 May 1990, when it finally became a faculty of the university.)
In 1920, the so-called Lex Mareš (No. 135/1920 Sb. z. a n.) was issued, named for its initiator, professor of physiology František Mareš, which determined that the Czech university was to be the successor to the original university. Dropping the Habsburg name Ferdinand, it designated itself Charles University, while the German university was not named in the document, and then became officially called the German University in Prague (German: Deutsche Universität Prag).
In 1921, the German-speaking Bohemians considered moving their university to Liberec (German: Reichenberg), in northern Bohemia. In 1930, about 42,000 inhabitants of Prague spoke German as their native language, while millions lived in northern, southern and western Bohemia, in Czech Silesia and parts of Moravia near the borders with Austria and Germany.
In October 1932, after Naegle's death, the Czechs started again a controversy over the insignia. Ethnic tensions intensified, although some professors of the German University were members of the Czechoslovak government. Any agreement to use the insignia for both the universities was rejected. On 21 November 1934, the German University had to hand over the insigniae to the Czechs. The German University senate sent a delegation to Minister of Education Krčmář to protest the writ. At noon on 24 November 1934, several thousand students of the Czech University protested in front of the German university building. The Czech rector Karel Domin gave a speech urging the crowd to attack, while the outnumbered German students tried to resist. Under the threat of violence, on 25 November 1934 rector Otto Grosser (1873–1951) handed over the insigniae. These troubles of 1934 harmed relations between the two universities and nationalities.
The tide turned in 1938 when, following the Munich Agreement, German troops entered the border areas of Czechoslovakia (the so-called Sudetenland), as did Polish and Hungarian troops elsewhere. On 15 March 1939 Germans forced Czecho-Slovakia to split apart and the Czech lands were occupied by Nazis as the Protectorate of Bohemia and Moravia. Reichsprotektor Konstantin von Neurath handed the historical insigniae to the German University, which was officially renamed Deutsche Karls-Universität in Prag. On 1 September 1939 the German University was subordinated to the Reich Ministry of Education in Berlin and on 4 November 1939 it was proclaimed to be Reichsuniversität.
On 28 October 1939, during a demonstration, Jan Opletal was shot. His burial on 15 November 1939 became another demonstration. On 17 November 1939 (now marked as International Students' Day) the Czech University and all other Czech institutions of higher learning were closed, remaining closed until the end of the War. Nine student leaders were executed and about 1,200 Czech students were interned in Sachsenhausen and not released until 1943. About 20 or 35 interned students died in the camp. On 8 May 1940 the Czech University was officially renamed Czech Charles University (Czech: Česká universita Karlova) by government regulation 188/1940 Coll.
The Second World War marks the end of the coexistence of the two universities in Prague. With the expulsion of Germans from Czechoslovakia at the end of the war, the German-speaking Charles-Ferdinand University was dissolved and many of its members were expelled. In 1956, they were allowed to establish a new Collegium Carolinum in Munich.
In 1945 the insignia of the university (the rector's chain, the scepters of the individual faculties, the university seal and also the founding documents and other historical documents) vanished. None of these historical objects has been found to this day.