Hunthausen was ordained a priest by Bishop Joseph Gilmore on June 1, 1946. He returned to Carroll College, where he served as a professor of chemistry and a football and basketball coach. In 1953 he earned a Master's degree in chemistry from the University of Notre Dame. He served as president of Carroll College from 1957 to 1962. He was named a domestic prelate in 1958.
Episcopal ministry
Helena
On July 8, 1962, Hunthausen was appointed the sixth Bishop of Helena by Pope John XXIII. He received his episcopalconsecration on the following August 30 from ArchbishopEgidio Vagnozzi, with Bishops Bernard Topel and William Condon serving as co-consecrators. As bishop of Helena, he was a Council Father at all four sessions of the Second Vatican Council. He was the newest and youngest American bishop at the start of the Council. Starting in 1976 Hunthausen worked with Call to Action and sought to implement their program. His tenure as bishop of Helena was marked by increased lay involvement in church matters, the establishment of a mission in Guatemala, the closure of several Catholic elementary and high schools, and the strengthening of religious education programs which function in every diocesan parish.
Seattle
He was appointed Archbishop of Seattle, Washington by Pope Paul VI in 1975. In 1982, Hunthausen withheld half of his income tax to protest the stockpiling of nuclear weapons and the Trident missile program which had a base nearby, in Puget Sound. In a speech, he said, "Trident is the Auschwitz of Puget Sound." This tax resistance prompted the Internal Revenue Service to garnish his wages.
Church investigation
As a result of the complaints surrounding his alleged deviations from church doctrine, in 1983 the Vatican authorized Cardinal Ratzinger, Prefect of the Congregation for the Doctrine of the Faith, to launch an investigation. Archbishop James Hickey of Washington, DC, was named apostolic visitor to the Archdiocese of Seattle. Hickey's delegation met with Hunthausen and others to investigate his administrative and pastoral practices. The investigation concluded that Hunthausen had exercised "weak doctrinal leadership" in a number of areas, including allowing children to receive the sacrament of Communion without first having received the sacrament of penance. Donald Wuerl, later Bishop of Pittsburgh and Archbishop of Washington, was controversially named an auxiliary bishop with special powers. According to Thomas Bokenkotter, "A resolution of the affair was finally announced by the Vatican in April after it accepted the report of a commission that recommended that Hunthausen's authority be restored and a coadjutor bishop be appointed. Hunthausen stoutly maintains that his archdiocese has remained fundamentally the same and was never in violation of Vatican doctrine; nor has he had to alter the general direction of his ministry or compromise his liberal beliefs." Thomas Joseph Murphy, Bishop of the Diocese of Great Falls–Billings was appointed coadjutor in 1987. Archbishop Hunthausen is remembered most for his support of the poor and disenfranchised. He was also a great advocate for the youth and encouraged better catechesis in Catholic parishes and Catholic parochial schools despite waning enrollment. In 1985, he helped establish the Institute for Theological Studies at Seattle University, which in 1996 evolved into the School of Theology and Ministry.
Retirement and Death
Archbishop Hunthausen retired on August 21, 1991, his 70th birthday and resided near Helena, Montana, with his brother, Father Jack Hunthausen. He continued to hear confessions once a week in East Helena, and led retreats in the Helena diocese. As of October 2011, Hunthausen was the last living American bishop to have attended all four sessions of the Second Vatican Council. On July 22, 2018, he died in his home in Helena at the age of 96. He is the second archbishop interred in the crypt at St. James Cathedral.