[3] Following ordination, McGuckian spent four years as a teacher in Clongowes Wood College and vocations director for the Jesuits, before undertaking a six month period of spiritual renewal in southern India and serving in a shanty town in Quezon City, Philippines.

[3] He returned to Ireland in 1992, where he was appointed director of the Jesuit Communication Centre, during which he developed Sacred Space, a website which allowed people to pray at their computer, in 1999, and Catholic news service CatholicIreland.net in 2004.

He also co-authored the drama 1912 - A Hundred Years On with Presbyterian historian Philip Orr in 2011, which looked at the experiences of the Ulster Covenant and the wider Home Rule movement from both nationalist and unionist perspectives.

[18] He also joined a number of church leaders in the West of Ireland on 16 September 2021, in calling on the Irish government to offer reparations to homeowners whose properties were affected by defective concrete blocks.

[19][20][21] In an interview with The Irish Catholic in February 2021, McGuckian took issue with the view held by political leaders that public worship was deemed to be "non-essential" during the COVID-19 pandemic in the Republic of Ireland.