The supreme decision-making body in HUS is the Council, which oversees the Executive Board. Operational activities are managed by the CEO.

The 24 member municipalities of the Hospital District and the University of Helsinki elect 55 members to the Council for each municipal electoral period.

The executive body of HUS, subordinate to the Council, is the Executive Board, appointed by the Council for the duration of its term. The University of Helsinki appoints a further two members to the Executive Board. 

The operational activities of HUS are managed by the CEO. The CEO of HUS up until July 31, 2021 was Juha Tuominen, who at that time retired on a disability pension. Chief Medical Officer Markku Mäkijärvi has been acting CEO since August 1, 2021.