The Museum collaborates with the University of the Aegean as well as with many other higher education institutions in Greece and abroad. The cooperation with the National and Kapodistrian University of Athens, the Aristotle University of Thessaloniki, the University of Patras and the University of Crete is particularly close.

Field visits and field exercises are organized for undergraduate and postgraduate students.

In collaboration with universities, diploma theses, master dissertations and doctoral dissertations are conducted. Summer educational schools and training programs are also organized.

Students' summer internship programs are held every summer.

The museum collaborates in the inter-university postgraduate programs:

• Natural Hazards and Disaster Mitigation (University of the Aegean, Aristotle University of Thessaloniki, National Observatory of Athens)

• Paleontology-Geobiology (Aristotle University of Thessaloniki, University of Athens, University of Patra, University of the Aegean, University of Crete)