[4][5] McDonagh was appointed Professor of Moral Theology and Canon Law at the Pontifical University at Maynooth in 1958, a post which he held until his retirement from full-time teaching in 1995.
[6] He was offered a permanent teaching position at the University of Notre Dame in 1979, but turned it down because he did not want to emigrate from Ireland.
[4][3] McDonagh was very critical about the Catholic Church's refusal to morally condone the use of contraceptives to prevent the spread of HIV/AIDS.
[7] One of his ex-students wrote, "In my opinion one of the greatest tragedies to befall the Irish Church in recent times, was its inability to harness the messianic qualities of Enda MacDonagh in a leadership role.
[11] McDonagh sat on the Senate of the National University of Ireland, and was part of the board of the Higher Education Authority.