Music history and music aesthetics were taught occasionally at the Friedrich Schiller University already during the nineteenth century. With the foundation of the Großherzogliche Orchesterschule in 1872 (Grand-Ducal Orchestra School), which was later to become the University of Music FRANZ LISZT Weimar, these subjects became an established part of the curriculum. In 1913, Fritz Stein was the first musicologist to be appointed associate professor at the Friedrich Schiller University. For a brief period during the further course of the twentieth century, both institutions established a joint department.

A few years after Heinrich Besseler's appointment at Leipzig in the time of the German Democratic Republic, however, the department—then located at Jena—was closed down. It was refounded at the University of Music FRANZ LISZT Weimar in 1990. The foundation for the programme in arts management, which was to be associated with the Department of Musicology, was laid in 1990/91. Following several attempts at restructuring the institution, the Department of Musicology has once more been hosted jointly by the University of Music Weimar and the Friedrich Schiller University since January 2000.