allinn University has 6 institutes, 2 regional colleges, 5 centres of excellence, 8 research centres and 13 support units. See the full list of units below.

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 is made up of vice-rector for academic affairs Priit Reiska, vice-rector for research Katrin Niglas, vice-rector for creative activities and cooperation Andres Jõesaar and the director of  finances Kurmet Ojamaa.

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.