He attended Cloonakilla National School in Bealnamulla and St. Aloysius College in Athlone, before studying for the priesthood at St. Patrick's Society for the Foreign Missions in Kiltegan, County Wicklow, and the Pontifical Gregorian University in Rome.

[2] After completing a licentiate in dogmatic theology in 1995, Duignan's first pastoral assignments were as a curate in the cathedral parish in Sligo and chaplain to the local Institute of Technology, before returning to Rome to complete doctoral studies in contemporary trinitarian theology at the Pontifical Gregorian University.

In the same year, he was also appointed chancellor, diocesan secretary and episcopal vicar for education and formation for the Diocese of Elphin, and subsequently as financial administrator in 2018.

[3][4][1][5] He received episcopal ordination from his predecessor, John Kirby, on 13 October in St Brendan's Cathedral, Loughrea.

[6] Following the announcement by Pope Francis on 16 November 2021 that the Dioceses of Clonfert and Galway, Kilmacduagh and Kilfenora would be united in persona episcopi, the first-ever union of its kind in Ireland[a], Duignan was appointed Bishop of Galway and Kilmacduagh and Apostolic Administrator of Kilfenora in addition to his appointment as Bishop of Clonfert on 11 February 2022.