McLoughlin was born in Cross Street in the centre of Galway City on April 9, 1929. His parents ran a small wholesale grocery business. He attended the Patrician Brothers primary school in Nuns' Island and St. Mary's College in Galway. He studied for the priesthood at Maynooth and was ordained on June 20, 1954. He then taught at St. Mary's College, Galway where he developed interests in basketball and amateur dramatics, and was appointed diocesan secretary in September, 1965. He became parish priest of the cathedral parish in Galway in 1983.
On February 10, 1993, when bishop Eamon Casey resigned, McLoughlin was appointed by Pope John Paul II as bishop of Galway. The formal ordination as bishop occurred on March 28. He served as chairman of the finance and general planning committee of the Irish Bishops' Conference.
McLoughlin announced his retirement on May 23, 2005, and on July 3 was succeeded as bishop of Galway by Martin Drennan. He lived in Claregalway during his retirement, and died on November 25, 2005 in Galway Clinic. His funeral was held in Galway Cathedral, and he was interred in the crypt beneath the cathedral.
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