The Board of the Estonian Research Council is the highest supervisory body which plans the activities of the Research Council, organises its management and carries out supervision. Members of the Board are appointed and removed by the minister for education and research. Their term of office lasts five years.
- Indrek Reimand – Estonian Ministry of Education and Research, Deputy Secretary General for Higher Education and Research; Chairman of the Board
- Teet Jagomägi – Member of the Board of Estonian Association of Information Technology and Telecommunication, chairman of the board of Regio Ltd;
- Joonas Pärenson – Advisor at the Ministry of Finance of the Republic of Estonia;
- Toivo Maimets – Professor at the University of Tartu;
- Kaupo Reede – Estonian Ministry of Economic Affairs and Communications, Director of Economic Development Department;
- Taivo Raud – Estonian Ministry of Education and Research, Head of the Research Policy Department
- Mart Ustav – Professor at the University of Tartu, Member of the Estonian Academy of Sciences