In 1878, Archbishop Peter R. Kenrick decreed that a mission church - to be named St. Paul - be established for the people of Fenton. A white frame building was erected on land previously owned by Samuel Vandover and the first Mass was celebrated on Christmas Day, 1879. The mission was served by Rev. John Feltman, who came by horse and buggy from Assumption Parish, Mattese, to celebrate the Eucharist every other Sunday.
Some time later, the mission was elevated to the status of a parish and Rev. James Kern was appointed the first resident pastor. In 1918, the cornerstone was laid for the brick church which still stands in "Olde Towne Fenton" on Main Street.

Three years after the brick church was dedicated, St. Paul Parish opened its first school. The building consisted of two classrooms, a multi-purpose room and a convent for the Sisters of the Most Precious Blood of O'Fallon, Missouri, who staffed the new school. Early in the 1950's, to accommodate an ever-increasing enrollment, some classes were moved across the street to the parish hall. This building had been built in 1926 and had provided the parishioners with a place to hold dances, wedding receptions, basketball games and various fund-raisers.

Following Fr. Kern, pastors who served the parish were: Rev. John Waeltermann, Rev. William Schulte, Rev. Mathias T. Sevcik, Rev. Joseph P. Kennedy, Rev. Patrick J. Doyle and Rev. Norbert Pohl. Rev. Edward H. Hrdlicka served as assistant pastor from 1941 to 1948, and after eight years as chaplain of St. Mary's Hospital, he returned as pastor in April, 1956.

The parish continued to grow along with the city of Fenton. Because of this expansion, land on which to build a new church/school building was purchased along New Smizer Mill Road (Hwy 141) on the site of the Hessoun Orphanage. The first Mass was celebrated on Easter Sunday, 1959.

In 1961, two houses were built in the Forest Knoll subdivision to serve as a rectory and a convent. Due to an increasing enrollment, the school building was enlarged in 1963 with the addition of eight classrooms. In 1972, a new rectory was built on the parish grounds just north of the school.

Permission was granted in 1983 to build the existing church on its present site. The space vacated in the school building was converted into a gym/cafeteria with the old cafeteria being divided into two new classrooms. The Most Rev. John L. May dedicated the new church on November 4, 1984.

Upon the retirement of Rev. Edward H. Hrdlicka in June l991, Rev. Richard Everding was appointed Pastor of St. Paul Parish. Rev. Everding served in that position for nine years until June 2000. Rev. Msgr. Michael Dieckmann was appointed Pastor and served the parishioners of St. Paul Parish for 18 years until June 2018.  Rev. Msgr. Kevin Callahan was appointed Pastor in June 2018 and is serving the parishioners of St. Paul Parish together with one Associate Pastor, Rev. Scott Scheiderer.