Controlling is a managerial activity, meaning that it is goal-driven and aims at guiding all decisions towards achieving goals. Controllers monitor the process of determining goals from start to finish, and share the responsibility for their achievement. Controlling is making its way into a new area, the public sector. Although its introduction into the public sector is being increasingly discussed by both the organisations and policy-makers, it will require taking into account specific features of the sector in which profitability or market shares are rarely the goal. When introducing controlling into the public sector, the specifics of the mission, goals and processes should be considered; the primary task of a public sector controller should be to clarify and precisely define these objectives. The introduction of controlling in the public sector is certainly justified, on account of the growing expectations of the public; as this sector has a particular importance for the society as a whole, it requires an active, target-oriented management. In Croatia, public sector controlling is at the very early stage of development. The aim of this paper is to examine the concepts of controlling and public sector, as well as to analyse public sector controlling in general. A particular emphasis is put on the possibilities of its implementation, by using the example of the Agency for Science and Higher Education. Scientific methods of induction and deduction, as well as descriptive and compilation methods, were used in the making of this paper.