Tallinn University has 6 institutes, 1 regional college, 5 centres of excellence, 8 research centres a 15 support units. See the full list of units below.

The Senate is the university's highest Board of Management and is vested with powers of decision-making and the Advisory Board acts in an advisory capacity.

Tallinn University is governed by the Rectorate – a body that assumes office for a period of five years under the management of the Rector who is elected according to a traditional academic procedure. Since 2011, the Rector is professor Tiit Land. The Rectorate's members are vice-rector for academic affairs Priit Reiska, vice-rector for research Katrin Niglas, vice-rector for sustainable development Helen Sooväli-Sepping, vice-rector for creative activities and cooperation Andres Jõesaar and the director of  finances Kurmet Ojamaa.