In 1365, Duke Rudolf IV already mentioned a library as publica libraria or gemaine půichkamer oder libreye in the founding document of the University of Vienna. The arts (philosophy) faculty library developed only slowly to become the most important of the faculty, college and student libraries and, in the fifteenth century, the main library. The importance of the University of Vienna declined considerably in the sixteenth and seventeenth centuries as a result of the Turkish wars and the plague epidemics. Because of the shortage of space, the university offered the contents of the library to the ruler Maria Theresa. In 1756 the old library was closed and its contents (2,787 volumes of manuscripts, printed matter, etc.) were transferred to the imperial court library. The new Academic Library, which opened in the Akademisches Kolleg building in 1777, included the book collections of the Jesuit order disbanded in 1773 and a large number of duplicates from the court library. The inventory of 45,000 books was considerably enlarged through the dissolution of the monasteries under Joseph II (1782–1787). The initial idea of having the new university library supervised by the court library gave way to the decision in 1775 to allow the library to remain an independent entity under the control of a "Studien-Hofkommission", which would appoint a library director. This administrative move meant that the university library was more closely attached to the university than before but that it would be independent from it in terms of acquisitions, staff and budget. This arrangement did not end until the reforms of the 1993 University Organization Act some 225 years later. Under the 2002 Universities Act, the university library was merged in 2004 with the archive of the University of Vienna and the former central, faculty, department and institute libraries were reorganized as subject-area libraries and a new service unit, the Vienna University Library and Archive Services was formed. The library's medical holdings were transferred to the newly founded Medical University of Vienna. In 1884 the university library with its 300,000 or so volumes and the University of Vienna itself transferred to a new building on the Ring designed by Heinrich von Ferstel. In spite of massive space issues, the library turned into the leading research library in the Austro-Hungarian monarchy and one of the largest in Europe in terms of readers (in 1912 it had over 293,000 users). The First World War marked the end of this phase. After the end of the monarchy, the former court library, now the National Library, increasingly replaced the university library as a state library. Renewed suggestions for a merger were rejected both by court library director Josef Donabaum and university library director Salomon Frankfurter. A decree by the Education Department in 1920 finally confirmed the autonomy of the two libraries.

The library scene not only in Vienna but in Austria as a whole underwent political changes at the start of the twentieth century. In the founding phase of the Republic of Austria a closer affinity to the German library sector developed. The Österreichischer Verein für Bibliothekswesen (Austrian Library Society) founded in 1896, one of the oldest professional librarian associations in the world, continued to exist until 1919. At the general meeting of the Verein Deutscher Bibliothekare (VDB) in 1920 in Weimar, the deputy director of the court library Othmar Doublier requested a change in the VDB statutes to enable Austrian colleagues to join the association. The motion was approved by the general meeting the following year. This meant that for the next twenty-five years, until 1945, the VDB represented Austria's professional interests—even after the VDB was "aligned" following the seizure of power by the National Socialists in Germany and its reorganization according to the "Führer principle" in 1935. At the time, the "National Socialist ideology" could not be anchored in the new statutes out of "consideration" for Austrian colleagues. In the late 1920s and during the 1930s the situation among Austrian librarians was politically fraught. In particular, conflicts between the German Nationals/later National Socialists and the Cartellverband came to a head. In 1933, Johann Gans, a member of the Cartellverband, was appointed director of the university library. As a result of the ban on the NSDAP at the time of the Austrofascist corporate state, four "illegals" were dismissed: Paul Heigl (from 1938 director of the National Library), Robert Hohlbaum (subsequently director of the city library in Duisburg), Rudolf Pettarin and Karl Wache. Paul Molisch, who also wrote clearly German Nationalist articles but had good connections in the Ministry of Education, remained in office.

The annexation of Austria to the German Reich brought with it the dismissal or forced retirement of around 20 per cent of the staff. Hildegard Braun, Rudolf Capka, Richard Czwiklitzer und Norbert Jokl lost their jobs for "race" reasons. Viktor Kraft, whose wife Johanna Kraft, née Wolf, was deemed a Jew under the Nuremberg Laws, and Robert Pistauer, a "first-degree Mischling", were forced to retire. Six other librarians were persecuted on political grounds, including Josef Sponer, Ferdinand Marass and Egon Hanel. Alois Jesinger, the former head of the catalogue department, who joined the NSDAP in May 1938, was appointed provisional director at the end of 1938 in place of Johann Gans. Rudolf Geissler, a National Socialist who had retained his position, and the re-recruited National Socialists Pettarin and Wache, who were subordinate to Jesinger, subsequently denounced him. It was not until autumn 1940 that the Reich Ministry of Education in Berlin confirmed his appointment. Jesinger assumed the position of director from March 1941. Gans remained in the university library for the time being before being demoted in 1939 to subject specialist and then, from 1943 to 1945, becoming director of the library at the Hochschule für Welthandel (now University of Economics and Business). Jewish students already suffered restrictions in their use of the university library right after the annexation. At the end of November 1938 the Reich Ministry of Economic Affairs, Education and Culture announced that Austrian Jewish students were to be denied admission to the university. In December 1938 Jews were banned from visiting the university library. This effectively halved the number of library users. During the Nazi era, the university library, like many other libraries, acquired expropriated assets particularly from Jews but also from political undesirables and institutions. In view of the increasing destruction through Allied air raids, the university library was ordered by the Reich Ministry of Education to secretly transfer almost its entire inventory of printed works (well over 1,200,000 items) to the National Library and to depots in the vicinity of Vienna, including Schloss Ernstbrunn, Schloss Horn (from April 1944), Gut Markhof in Schonfeld-Lassee, Schloss Mittergrabern near Hollabrunn, Burg Niederranna near Krems (until April 1944), die Rosenburg (from April 1944), Gut St. Christoph near Gloggnitz, Schloss Stetteldorf near Korneuburg, Therasburg near Horn and Schloss Wald in Pyhra near St. Pölten. In early 1945 library operations practically came to a standstill and regular work became impossible.

After the war, the former director Johann Gans was reinstated. The first post-war years were devoted to the reconstruction of the library. Around 10 per cent of the books had been lost or damaged in transport, through inadequate storage or other war-related complications. Looting during the Nazi era was extensively disregarded in the post-war period and restitutions were made to only a few previous owners. Alois Jesinger, who had been library director during the Nazi regime, was dismissed and charged with investigating "abandoned" looted books in the book-sorting office at the Austrian National Library. Over 151,000 items, later named the Tanzenberg collection, were transferred in 1951 in this way from the book-sorting office to the university library. An agreement between the Republic of Austria, the Jewish Community and the Jewish National and University Library (JNUL) in November 1955 organized the distribution of the books in a ratio of 60:40 between the university library and the JNUL. Approval was not given by the Sammelstelle für erbloses Vermögen (collection point for unclaimed assets) until 1960, and the books were gradually incorporated in the university library inventory over several decades. No investigation was made of the original owners of these books held in trust.

The systematic provenance research initiated in 2004 has now been extended to the university archive and University of Vienna collections and is part of the diverse research and memory projects at the university. In view of the multi-tiered library system, the precise number of libraries and book collections between 1933 and 1945 can no longer be determined. Apart from the university library (present-day main library), there were institute and seminar libraries, the libraries of university-based research institutions, private libraries and various collections. The Philosophy Faculty alone had at least fifty-one library collections at this time. Apart from the main library, initial findings are available for the Art History, English and American Studies, European Ethnology, Jewish Studies, Music, Middle Eastern Studies, Philosophy and Psychology and Theatre libraries, for the University Archive and for collections from the departments of Egyptology, Music and Zoology, which have been shared with the public in three international conferences (2008, 2013 and 2017), numerous publications, lists of works in public catalogues and on a website. By the end of 2018, twenty-five restitution cases involving around 2,250 print works, five plaster casts and a fractional literary estate have been carried out by the library. Heirs are being sought in a further twenty-two cases, while twenty-four suspicious cases proved to be legitimate acquisitions.