The Department for Folk Music Research and Ethnomusicology at the University of Vienna was founded in 1965 as the Department for Folk Music Research. It was the second such Department at an Austrian music university (which were known at that time as music academies). The founder of the Department, the university professor Walter Deutsch, was the Director of the Department until 1991 and Professor of the History and Theory of Folk Music.
The work carried out at the Department was in the tradition of the Viennese School of Folk Music Research. Research and teaching thus concentrated on Austrian vocal and instrumental folk music.  From the 1980s onwards, Rudolf Pietsch established research into styles of instrumental folk music and practical approaches which have had a continuous effect since then.
In 1994, after her appointment as a Professor, Gerlinde Haid also became Director of the Department.  The previous work of the Department was continued and gradually extended by a critical orientation towards cultural developments in society, areas of research and the range of methods used.
The music of minorities became an important subject area. International cooperations were intensified and the PhD programme was established. In 2001, Ursula Hemetek completed her habilitation (qualification as a university lecturer) in the subject of ethnomusicology. These developments led to ethnomusicology being included in the name of the Department in 2002. In 2003, the Research Centre for European Multipart Music was established at the Department. Under the leadership of Gerlinde Haid the Department also developed into an internationally recognised research institution and played a leading role in the organisation of the ICTM World Conference in 2007.
On 1 January 2011, Gerlinde Haid passed on the directorship of the Department to Ursula Hemetek, who was thus able to take over a well-run organisation.
In 2012 Ulrich Morgenstern took on the Professorship of the History and Theory of Folk Music.