Bishop Harry Flynn took over responsibilities as fourth Bishop of Lafayette in May, 1989, when Bishop Frey retired. As Ordinary, Bishop Flynn conducted parish and school visitations, encouraged vocations to the priesthood and religious life, promoted Catholic education and expanded religious education.
Along with Bishop Frey, he joined other Louisiana bishops in pastoral letters condemning capitol punishment, warning of the evils of gambling, opposing abortion, supporting Catholic schools, and promoting financial support of the Catholic church.
In February, 1994 Bishop Flynn was appointed Coadjutor Archbishop of St.Paul-Minneapolis in Minnesota and assumed those duties in April, 1994. Upon the retirement of Archbishop John Roach, he became the seventh Archbishop of St. Paul-Minneapolis on September 8, 1995. Archbishop Flynn retired as Archbishop on his birthday, May 2, 2008. After a long battle with bone cancer, Archbishop Flynn died at the age of 86 on September 23, 2019.