After his philosophical and theological training at the Gozo Major Seminary, Fr Farrugia did post-graduate studies in theology obtaining an S.Th.L. in Dogmatic Theology and his doctorate in Fundamental Theology at the Pontifical Gregorian University, Rome. He also studied philosophy at the Lateran University and Islamology at the Pontificio Istituto di Studi Arabi e Islamici (P.I.S.A.I.). In 1983 he became a lecturer in theology at the Sacred Heart Major Seminary of Gozo, and in 1988 he joined the Faculty of Theology at the University of Malta where he still lectures in fundamental theology and ecumenism.  Mgr Farrugia has also given courses in Mediterranean civilizations and religions. On behalf of the new University of Malta's Gozo Centre, Dr Farrugia coordinated several highly successful series of public lectures focusing on the history and culture of the island. He is the author of The Church and the Muslims and contributor to various international theological publications. After a ten-year term as archpriest at St George's basilica in Gozo, in 2008 Mgr Farrugia was appointed representative of the Maltese Bishops' Conference to the Conference of European Union Bishops (COMECE) and delegate for culture in the diocese of Gozo.