He then served on the faculty of Loras College until 1941, when he became a pastor in Osage and afterwards in Elkader. On August 3, 1946, Pope Pius XII appointed Fitzgerald auxiliary bishop of the Dubuque Archdiocese, and he was ordained a bishop on September 12, 1946. On October 20, 1949, Pope Pius XII appointed Bishop Fitzgerald Bishop of the Winona Diocese; he retired on January 8, 1969.
He became known as "the building bishop" for his oversight of the construction of a cathedral, seminary, and several churches in the diocese. He attended all four sessions of the Second Vatican Council between 1962 and 1965, and subsequently implemented the Council's reforms in the diocese, including introducing English into the Mass.