The institution was founded in 1988 by Gerald Mader in his capacity as president of the ASPR, with the support of European UNESCO commissions, and is affiliated to the Austrian Study Center for Peace and Conflict Resolution (ASPR), also located at Stadtschlaining.

The original curriculum of EPU was designed along the lines of Johan Galtung’s ”Plan for a Master of Peace and Conflict Resolution” which he developed for the University of Hawaii.

The EPU's UNESCO Chair on Peace, Human Rights and Democracy was established in 1996.

In July 2013, EPU's accreditation was withdrawn by Austria's accreditation body; students currently enrolled in the "Master of Arts in Peace and Conflict Studies" programme may finish their studies until 2014.

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