He later attended the Pontifical North American College in Rome, Italy where he was eventually ordained.

On 30 December 1954 Pope Pius XII appointed Maloney the auxiliary bishop of the Roman Catholic Archdiocese of Louisville; he served in the capacity for 51 years.

He was consecrated as a Roman Catholic bishop in 1955 by Archbishop John Alexander Floersh at the Cathedral of the Assumption in Louisville, Kentucky.

He was influential in the passage of Dignitatis humanae (Declaration on Religious Freedom), one of only sixteen documents generated by the council and approved by the Pope.

Ironically, Bishop Maloney often said the traditional Latin Mass during his retirement at Saint Martin of Tours Church in Louisville.