In the early 1840’s, Irish immigrants settled in and near the Madison isthmus and founded St. Raphael Parish.  The first recorded act of this new parish was the celebration of the Holy Sacrifice of the Mass by Father Martin Kundig in the territorial capital of Wisconsin on August 15, 1842.  Governor J.D. Doty, a friend of Fr. Samuel Mazzuchelli, OP, donated land for a church on West Main Street between Fairchild and Henry.  Frs. Adalbert Inama and Max Gaertner and other visiting priests offered Mass in homes and in the new State Capitol.  Father Robert D. Whitehead was appointed the first pastor, remaining six months in 1848, the year Wisconsin became a state of the union.

The first church, a modest 20 by 24 foot frame building, was constructed in 1850.  In 1853, Father Francis Etchmann began work on the church building that stood for a century and a half.  The cornerstone was laid in 1854.  Archbishop John Henni of Milwaukee dedicated the new church, but it was not ready for use until 1862.  The cost of the project at that time was $30,000.  It was during the pastorate of Father Patrick Pettit in 1885 that a bell tower and spire were constructed at a cost of $8,000.

A modest frame structure erected in 1850 served as the first parish school.  In 1870 a three-story school building at the corner of Henry Street and West Washington Avenue replaced the first school.  In 1871, the Dominican Sisters from the Sinsinawa Mound arrived, welcomed graciously by the parishioners.

The German-speaking Catholics of Madison – desiring to hear a sermon and confess in their native language – began Holy Redeemer Parish in 1857.  The great influx of Irish settlers required another parish for them as well.  Therefore, St. Patrick's was founded in 1888 to serve English-speaking Catholics east of the Capitol Square.

By decree of Pope Pius XII, dated December 22, 1945, the Diocese of Madison was carved out of the eleven southern and western counties of the state.  St. Raphael Church, the original Catholic church in the city of Madison, was chosen as the cathedral of the new diocese.  Msgr. William Mahoney was the proud rector.

Bishop William Patrick O’Connor was installed as the first Bishop of Madison on March 12, 1946.  In September, 1953, the work of renovating the Cathedral was begun.  After the completion of this work, the renovated Cathedral was blessed by Samuel Cardinal Stritch, Archbishop of Chicago and former Archbishop of Milwaukee, on March 10, 1955.

Under the direction of Msgr. Edward Kinney, a new rectory and school were built in adjoining buildings along Henry Street, between West Main Street and West Washington Avenue. The rectory was built to accommodate a pastor, three associates, a live-in housekeeper and several guests.  There were ten Dominican Sisters in the school.

After the spring 1970 semester, the parish school closed for lack of students as few young families remained on the isthmus.  The building was sold in December 1971. A small religious education program continued.

In November, 1996, the Cathedral opened its basement as Shelter III for homeless men as a part of the Madison Transitional Housing Program.

In 2003, Bishop Robert Morlino was appointed as Bishop of Madison. Bishop Morlino gave the cathedral new prominence by frequently celebrating Sunday morning Mass there. Also in the summer of 2003, St. Raphael Cathedral was linked to Holy Redeemer Parish under the care of Msgr. Paul Swain.

In the fall of 2004, the 150th anniversary of the building of St. Raphael was celebrated. Soon after, in the fall and winter of 2004, a new copper and stainless steel steeple replaced a badly deteriorating wooden steeple.  The parish was just beginning to enjoy the new steeple when – early in the morning of March 14, 2005 – a fire set by an arsonist spread from the choir loft throughout the church.  The entire roof burned and caved in, but the steeple withstood the fire.

After the fire, the three parishes around the Capitol Square were linked under the care of a single pastor, with Cathedral Parish Masses being celebrated at Holy Redeemer and the offices being consolidated with those of St. Patrick.

On August 31, 2006, the Holy See announced that Msgr. Paul Swain was to become the eighth Bishop of the Diocese of Sioux Falls, South Dakota.

The current rector, Kevin Holmes, was then assigned as pastor of the linked downtown parishes.  He began duties on October 22, 2006.  In March of 2007, Bishop Morlino announced that Fr. Holmes had been named a prelate of honor, with the title Monsignor.

Corpus Christi 2007 was celebrated with a Eucharistic Procession from St. Patrick Church to the site of St. Raphael Cathedral. At the conclusion of that procession, Bishop Morlino announced his intention to build a new and larger Cathedral on a site including the location of the old church.

In October 2007, Bishop Morlino announced that St. Raphael Parish would be merged with the other two historic isthmus parishes to form a new Cathedral Parish community. This merger took place on July 1, 2008.

In June 2011, the building that had housed St. Raphael School was repurchased in order to have as large a site as possible for the eventual construction of a new cathedral church and related buildings.  Shortly thereafter, the former rectory and school buildings were demolished, and a new Way of the Cross installed on the entire site.

The principal home of the newly merged parish will eventually be a new cathedral to be constructed on the West Main Street site of old St. Raphael. Pending the completion of this project, the Cathedral Parish uses the churches and other facilities at the Holy Redeemer and St. Patrick sites.