Cooperation with Israeli universities and dealing with Jewish history and contemporary culture in research and teaching at Freie Universität Berlin have both been important to Freie Universität since the 1950s. From the beginning, the collaboration in research and teaching covered all the subject areas, including medical training.

Shortly after the university was founded in 1948, the faculty and management undertook efforts to gain Jewish emigrants as visiting professors for the university. One of the first of these was the New York-based German studies scholar, Adolf Leschnitzer. During the first years after Freie Universität was founded, numerous other emigrants who had returned to Germany were hired at Freie Universität Berlin, including Ernst Fraenkel, a professor of political science, and Ernst Hirsch, a professor of law and intermittently rector and deputy rector of the university

In 1963 the first  Institute of Jewish Studies in Germany was founded at Freie Universität. The decision to establish this institute was made in connection with the appointment of Jacob Taubes, who later became the first director of the institute.

The idea of creating an institutional framework for academic contacts to the Hebrew University of Jerusalem was already in place in 1957, as indicated by a letter, which is currently in the University Archives. An official partnership agreement between the two universities was concluded in 1986. In the meantime, they are cooperating within a strategic partnership, which includes numerous joint research projects in the natural sciences, humanities, and social sciences as well as student exchange.