The highest decision-making body of the university is the eleven-member University Council, which holds responsibility for the university's economic activities and long-term development, adopts the university's statutes and approves its budget.

The council comprises 11 members, of whom five are nominated by the Senate (the members for the first new Council were nominated by the previous University Council), one by the Estonian Academy of Sciences (whose nominee can not be an employee of the University of Tartu) and five by the Minister for Education and Research (who is under a duty to seek public advice on his/her nominations and whose nominations should seek to ensure that a majority of council members are not employees of the university).

The members of the Council are approved for a term of five years by the Cabinet of Ministers of the Republic of Estonia upon a proposal of the Minister for Education and Research. The Cabinet of Ministers approved the nominees for the first Council on 22 December 2011.

The members of the new Council are:

Nominees of the University of Tartu:
Toomas Asser, Head of the Nerve Clinic of UT Hospital, Professor of Neurosurgery
Toivo Maimets, Director of UT Institute of Molecular and Cell Biology, Professor of Cell Biology
Peeter Saari, Head of the Laboratory of Physical Optics, Professor of Experimental Physics, Academician
Jüri Sepp, Professor of Economic Policy, Vice Dean for Development of UT Faculty of Economics and Business Administration
Paul Varul, Head of UT Institute of Private Law, Professor of Civil Law

Nominee of the Estonian Academy of Sciences:
Kari Olavi Raivio, Professor and former Rector of the University of Helsinki

Nominees of the Minister for Education and Research:
Kaja Tael, Undersecretary for EU Affairs of the Ministry of Foreign Affairs
Toomas Kiho, Editor-in-Chief of Akadeemia, Advisor to Prime Minister of the Republic of Estonia
Kersti Kaljulaid, member of the European Court of Auditors
Vahur Kraft, Head of Estonian division of Nordea Bank
Aku Sorainen, founder and senior partner of the law firm Sorainen

The e-mail addresses of the members of the council, just like for all the University staff, follow the formula firstname [dot] surname [ät] ut [dot] ee. Should the names contain any umlauts or the Estonian-specific õ-character, they will modified as follows: õ->o, ä->a, ö->o, ü->u.

Additional information: Ivar-Igor Saarniit, Academic Secretary, ivar [dot] saarniit [ät] ut [dot] ee