The highest deliberative body in HUS is the Council. 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 day-to-day operations of HUS are managed by the CEO.