In 1985 he achieved the habilitation at Cologne for a work entitled, Untersuchungen zur Geschichte und Struktur des Aitolischen Bundes (Research on the History and Structure of the Aetolian League).
In addition, Funke is leader of the research project Historische Landeskunde des antiken Griechenland (Historical Study of Ancient Greek Regionalism) and since 1991 has been Pro-rector for Teaching and Student Affairs at the university of Münster.
Funke's research focusses are the history of the Greek state system from Mycenaean to Roman times, Greek historiography, ancient constitutional history, ancient regionalism and historical geography, as well as the relationship between religion and rulership in antiquity.
Funke was pro-rector for Teaching and Student Affairs at the University of Münster, as well as a member of the Joint Academic Reform Commission of North Rhine-Westphalia and of the working group, "New Media in Higher Education" of the German Rectors' Conference.
He is also a board member and managing director of the Institute for Interdisciplinary Cypriot Studies at the University of Münster.