He became curate of Carlow in 1979, a post he held until 1981 when he was appointed Librarian of Pusey House, Oxford and Fellow of St Cross College.
He has been a champion of ecumenical dialogue and during his time a Roman Catholic and a former Moderator of the Presbyterian Church were elected to the cathedral's 24-person Chapter.
[5] After expressing doubts concerning the validity of some New Testament verses in our modern world, questions were raised over Dr. MacCarthy's claimed orthodoxy.
[8] In April 2008 in a letter to The Irish Times he referred to Muslims and Hindus as indoctrinating their children into "a cult".
In 2011 he invited all seven presidential candidates to support his suggestion that St Patrick's should become a national ecumenical cathedral for all Christians in Ireland.