Agency theory is a theoretical platform used primarily to describe processes related to corporate governance. However, the theory is also being used to describe the processes associated with the functioning of the higher education system. Contractual relationships in this sector make it possible to identify the institutions that may act as either principal or agent, depending on the research perspective. Relationships between the state/government (principal) and public universities (agents) are the most commonly studied paradigm.The aim of this article is to present proposals for reform of the higher education system in Poland, using agency theory as the research perspective. The most important dysfunctionalities of the current system, viewed as a manifestation of the agency problem, are identified, and the proposed new standards of academic governance are confronted with theoretical mechanisms reducing conflicts of interest: outcome-based and behaviour-based contracts. The main recommendation contained in reform proposals is a desire to increase the institutional autonomy of public universities, leading to a strong leadership of the university authorities.