Roman Catholicism had its early beginnings in Madison about the time the city was founded in 1880. Catholic missionaries visited periodically before a resident pastor was assigned. Among them were Father John Brogan and Father S.S. Mattingly. Father Thomas Flynn, the first resident pastor, was the actual founder of St. Thomas Aquinas Church, which he named after his patron saint.
Father Flynn came to the Territory as a young seminarian from Milwaukee, WI, and was ordained by Bishop Marty as one of the first priests of the Territory. During his 45 years here, he received the title of Monsignor and Protonotary Apostolic. He served as Vicar General of the Diocese under Bishop O'Gorman.
Father E.J. Egan then came to St. Thomas. Shortly after his arrival, he began laying plans for the establishment of a parish school. In the fall of 1928, a modern brick building costing $100,000 was dedicated. The school included grades 1-12. A home for the Presentation Sisters who staffed the school was also provided.
Father J.M. Reuter of Colman was transferred to Madison where he remained for 16 years. Following the scarcity of WWII, Father Reuter did much to improve and expand church property. He lifted the $80,000 debt against the school. The high school was eliminated and the second floor redesigned to accommodate the Sisters.