Strategic management is the responsibility of the Board of University of Aarhus while day-to-day management is the responsibility of the Director General according to authorisation from rector. The scientific activities are organized under eight research departments.

The departments are centred at three locations: Roskilde near Copenhagen, Silkeborg in Jutland and Kalø in Jutland. The centres comprise fully equipped modern laboratories and facilities built in 1991 or later. These meet all relevant safety requirements in connection with the handling of toxic substances and genetically modified microorganisms and plants. Small research plots are available at Roskilde and Silkeborg while large research areas covering agricultural fields and woodlands are available at Kalø.