The Fondazione Politecnico di Milano is run by a Board of Directors made up of 12 members, of which six are appointed by the Politecnico (including the President), five are appointed by the other Founder Members and one is appointed by the Italian Minister for Education, University and Research. At meetings of the Board of Directors, the Chancellor of the Politecnico di Milano and the Chairman of the Founder Members' Assembly attend ex officio, without voting rights. The Board is responsible for the ordinary and extraordinary administration of the Fondazione.

Setting out the guidelines for the Fondazione's activity and its objectives and programmes, appointing the General Manager, administering the institution's assets and approving the draft financial statements are some of the most important duties performed by the Board of Directors.