[2][3] Returning to Victoria, McKenna was appointed an Assistant Priest in the parish of St Joseph's, Warragul in the Diocese of Sale before moving to an administrative role as Bishop's Secretary, Diocesan Secretary and Chancellor where he was a regular columnist in the diocesan monthly newspaper, Catholic Life.
While undertaking postgraduate studies from the Gregorian University in Rome, in 1991 McKenna was elected as General Secretary of the Australian Catholic Bishops' Conference, based in Canberra.
During 1998 he was Administrator of Lumen Christi Parish, Churchill before taking up a Resident Fellowship in the Divinity School of Harvard University.
[2][3] Serving as rector of Corpus Christi College from 1999 until 2005, McKenna established strong links between the Seminary and the Catholic Church in Vietnam.
[2] In 2006, McKenna was appointed as Catholic Chaplain to the University of Melbourne, where it is reported he reintroduced the celebration of Mass on campus and started new groups in social service, biblical study, Christian meditation and philosophy and faith.