The ISEK directorate manages and represents the institute and its interests towards the university and the public. It is composed of the two departments of Social and Cultural Anthropology, and Popular Culture Studies. The Ethnographic Museum has its own directorate, which is equivalent to the ISEK directorate in museum-related decisions. The two co-directors are, at the same time, also the respective study program directors. The ISEK directorate is appointed by the Excutive Board of the University for a period of four years at the request of the institute's assembly, a re-election is possible.
Each department of the ISEK has a management which supports the co-directorate and assumes coordination on a department level and across departments.