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 – Chairman of the board of Reach-U;
- Jaanus Karv – Advisor at the Ministry of Finance of the Republic of Estonia;
- Toivo Maimets – Professor at the University of Tartu;
- Jakob Kübarsepp – Professor at the University of Tartu, Member of the Estonian Academy of Sciences;
- Anu Toots – Professor at Tallinn University.