The first students were accepted in the PhD programme at the Estonian Academy of Arts in 1995. The first doctoral theses were defended in the same year by external students (see the defended theses). In 2002, the curricula for architecture, art history, as well as cultural heritage and restoration were accredited.
In 2005, the Doctoral School was established at the Estonian Academy of Arts and a New Media and Design curriculum was added (since 2007, the Art and Design curriculum).
The decision-making bodies for the EAA doctoral studies and research in general are the board of the Doctoral School and the EAA Research Council.