The beginnings of St. Patrick Parish, the mother Church of Eau Claire, can be traced to the 1850s. Formed from St. Peter's Mission, it became St. Patrick Parish in 1865. The first church was located on what is now North Barstow Street. In 1882, Fr. John G. Collins completed a new church building in the remote uninhabited wilderness on the west side of the Chippewa River. A parochial school was located in the basement of the church. St. Patrick Parish began formalized Catholic education in Eau Claire.

On October 7, 1884, the church was destroyed by fire. Fr. Collins was returning from Menomonie and saw the flames from the train. Fire trucks had to be transported by ferry since the river was at flood tide. A young boy, James Campbell (later St. Pat's first priest-son), rescued the Blessed Sacrament. On June 21, 1885, the cornerstone of the new church was laid. This is the same church in which we worship today.

In 1889, Fr. Thomas A. Kelley and Fr. A.B.C. Dunne arrived in Eau Claire. Fr. Kelley died in 1891 and is buried alongside the church. Fr. Dunne invited the Benedictine sisters to run the school in 1892. A new school was erected in 1906, a convent in 1909 and rectory in 1914. Fr. Casper Dowd added a High School in 1930 with $30,000 left by James Holden, a lumber camp cook and operator of a boarding house at Porter Mills. Msgr. J. Francis Brady presided over the completion of Regis High School in 1953 and the formation of Calvary Cemetery in 1965. St. Patrick School continued with education of middle and elementary school students. Fr. L.B. Keegan established the first Parish Council in August, 1968, with Francis Wilcox as chairman.

Under Fr. Bernard McGarty, the church was renovated and won 17 architectural awards. Fr. John Heagle began Project 100 in 1983, installed a new Moller organ and established a new Lay Ministry program. In 1987 under Fr. Charles Hiebl, St. Patrick School became a middle school, and with St. Olaf, St. James and Sacred Heart Parishes, formed the Eau Claire Coordinated School System.

Under Fr. John Steiner, on January 1, 1999, St. Patrick Parish united with Sacred Heart Parish to become Sacred Heart of Jesus - Saint Patrick Parish. Fr. Paul Gitter became pastor later in 1999. With Fr. William Dhein as pastor, the Benedictine Room in the Parish Center was dedicated as a Chapel in 2008. Fr. George Thayilkuzhithottu, MSFS, became pastor in 2012. In January of 2015, Deanery Eucharistic Adoration began in the Benedictine Chapel. Fr. Brian Jazdzewski became pastor in 2018.