The Zweigbibliothek für Geschichte der Medizin (history of medicine branch library), part of the Universitätsbibliothek der Medizinischen Universität Wien (University Library of the Medical University of Vienna), is located in the Josephinum at Währinger Straße 25 in Vienna's 9th district. It has around 500,000 volumes and is the largest archival library of the history of medicine and related disciplines in Austria. It was founded on the initiative of the medical historian and psychiatrist Max Neuburger, founder of the Institute of the History of Medicine. After the Ministry of Culture and Education had issued a decree on 23 July 1906 approving the establishment of an institute for researching the history of medicine, Neuburger began to compile a medical history collection and library, located temporarily after the establishment of the institute in 1914 in the 1st Medizinische Klinik. Following on from a similar institute established in Leipzig in 1905, the Viennese Institute of the History of Medicine was the second oldest of its type in the German-speaking world. It was not until Julius Tandler, deputy state secretary in the public health department, proposed a separate location that the library was moved in 1918 to the Josephinum. Together with the stocks of the former medizinisch-chirurgische Josephsakademie (Josephinum Military Academy of Surgery) founded in 1785 by Joseph II as a training institution for military surgeons and the Wiener medizinisches Doktoren-Kollegium, the medical history library formed the basis for the present-day Zweigbibliothek für Geschichte der Medizin at the Universitätsbibliothek der Medizinischen Universität Wien. The library was further expanded through gifts from private individuals and institutions and through legacies. Today many other historical libraries are located there, including the Bibliothek der Gesellschaft der Ärzte in Wien (library of the College of Physicians in Vienna), the Obersteiner Library (Institute of Neurology) and the Max and Margareta Wolf Dermatology Library, the Reuter Endoscopy Library, and stocks of formerly dispersed medical institutes, university clinics and extramural establishments, Viennese hospitals and private legacies. The Bibliothek des Institutes für Geschichte der Medizin was subsumed in 1975 in the University of Vienna library and in 1986 in the Medical Faculty library at the University of Vienna. Since 2003 the Zweigbibliothek für Geschichte der Medizin has been part of the Medical University of Vienna library.

Directly after the annexation in March 1938 and the expulsion of Max Neuburger, head of the Institute of the History of Medicine, Rudolf Geissler, a librarian at the University of Vienna library, was appointed temporary administrator there. On 22 January 1940 the Cologne doctor, medical historian and Nazi Fritz Lejeune became director until early April 1945. During this time the stocks were considerably enlarged through purchases from antiques dealers. Lejeune's far-reaching plans for enlarging and restructuring the institute were helped by the fact that the institute received appreciable subsidies from the state (in particular the Ministry of Internal and Cultural Affairs), making it possible for extensive purchases to be made. Through the ideological upgrading of medical history under the Nazis and its introduction as an examination subject for medical students in 1940, the institute and library gained in importance as a means of providing ideological underpinning for future doctors. To enlarge the library Lejeune made use of his contacts with numerous antiques dealers in Germany and Vienna, including a number who had been involved in the Nazi book looting, such as Antiquariats- und Exportbuchhandlung Alfred Wolf in Vienna. On 1 November 1943 most of the library's books and instrument collections were moved to the property of Mautner-Markhof in Gänserndorf, Lower Austria, to protect them from air raids. From there the Red Army transferred them to the University of Vienna library, and they were returned in July/August 1946 to the Institute of the History of Medicine in the Josephinum. Lejeune transferred a smaller number of books towards the end of the war to Rainer-Spital. They were returned to the library in 1945. The paintings in the Josephinum were transferred in 1943 to Tullnerbach-Pressbaum and also returned to the Josephinum in 1945.

After Fritz Lejeune fled in April 1945, Leopold Schönbauer, head of the 1st Chirurgische Universitäts-Klinik in the Allgemeines Krankenhaus (General Hospital) and future rector of the University of Vienna, directed the institute, on a provisional basis at first, until 1960. The work at the institute and library was led by the medical historian Marlene Jantsch (1917–1994). From 1960 to 1979 the institute was headed by the medical historian and classicist Erna Lesky (1911–1986).