As far back as 1860, Masses were said in homes in the Milton area by priests who would come from surrounding towns. On the north end of the village of Milton Junction, a 30 x 60-foot building, with a tower was built in 1892 at a cost of $1,492. In 1894, Saint Mary Church of Milton Junction became a mission church of Saint Joseph in Fort Atkinson with Father F.X. Schneider as pastor. He sometimes had sermons in German and came by bicycle, train or horse and buggy. The church registry at that time had 45 names.

In 1911, after several different priests, Father McGinnity was the first resident pastor. Father Roche became pastor in 1921 and died as a result of an accident in 1922. From 1922 to 1933 Father Joseph Ryan was pastor until his death. Father F.X. Schneider then returned as pastor until his retirement in 1944. He was followed by Father Brill who saw the need to expand. Land, on Hwy 26 (this would later become Parkview Drive), was purchased in 1946. Groundbreaking was held in 1952. On May 17, 1953 the 8:00 a.m. Mass was the last Mass held in the church at the Junction and the 10:00 a.m. Mass was the first mass held in the new church in Milton.
 

Father Michael Jacobs became pastor in 1954 and in 1967 undertook the building of a “Center” for use as a church hall for religion classes. In 1968, Father James McEnery became pastor until his retirement in June, 1999. Under his direction, the church was remodeled and enlarged in 1988. He was followed by Monsignor James Uppena, who was the pastor until his retirement in 2013. Father Dave Timmerman was the next pastor and the first time that St. Mary Parish was required to share a priest with another parish. Father Timmerman was also the pastor at St. Joseph in Edgerton. After some serious medical issues, Father Timmerman was transferred by the bishop in October of 2019 to St. Pius in Cambridge and Father David Wanish became pastor of both St. Mary, Milton and St. Joseph, Edgerton. July, 2023 St. Mary, Milton became a member of Pastorate 14, along with St. Joseph, Fort Atkinson, St. Pius X, Cambridge, St. Francis of Assisi, Jefferson, St. Mary, Palmyra. Msgr. Donn Heiar is our pastor.