The University is led by the president. She is supported by three vice presidents and the chancellor. Together, they form the Presidium, which is responsible for all matters for which no other responsibility has been assigned in the Foundation Charter or the KU Basic Rules. The Presidium runs the daily operations of the University.

The legal body supporting the KU is the foundation bearing the same name, an ecclesiastical foundation under public law. The Catholic University of Eichstätt-Ingolstadt Foundation was established by the Bavarian dioceses in 1968 as the “Stiftung Pädagogische Hochschule Eichstätt” and renamed to “Kirchliche Gesamthochschule Eichstätt, Kirchliche Stiftung des öffentlichen Rechts” in 1972.