St. Joseph parish was organized in 1879 by Fr. Anton Pauck, as a mission of St. Mary's parish in Glasgow, MO. The first church building was blessed on November 5, 1890, and placed under the patronage of St. Joseph. St. Joseph became a parish in 1900 with Fr. Joseph Kroeger as the first pastor. Unfortunately around 1908, with the construction of the new parish, Sacred Heart, in New Franklin, MO, St. Joseph lost the opportunity for a pastor and returned to mission status under Sacred Heart, with Fr. Con Kane as pastor.

Then shortly after 1920, St. Joseph was closed, due to a very small congregation. On the contrary, it was during this time that Sacred Heart in New Franklin continued to grow, to the point they converted the former public school building into a church and parochial school, with classes beginning in 1936. The following years were a struggle though and in 1952, Sacred Heart School was forced to close its doors.

The time between 1952 and 1979, the Catholic Catechism was taught under the direction of the Sisters from St. Joseph's Hospital in Boonville, MO; then from Saints Peter and Paul in Boonville, MO, along with St. Mary's School in Glasgow, MO.

In 1954, Joseph Ritter, Archbishop of St. Louis expressed a desire for a new church in Howard County, and Fr. Thomas Sullivan was appointed pastor. Groundbreaking for the new St. Joseph Catholic Church took place in Fayette just two weeks after Easter in 1956. The finished church was dedicated at the Midnight Mass on Christmas of 1956.

Under the guidance of Fr. Sullivan, the parish grew and an additional resident living space was added to the rectory. An open house and rededication ceremony was celebrated on March 17, 1963. Between the years of 1963 and 1979, St. Joseph was blessed with continuity and strength.

Unfortunately, in 1978 Fr. McDonnell retired and with the shortage of priests for the area forced St. Joseph to once again be placed at mission status. Fr. William Flanagan and Fr. Thomas McGrath from St. Peter & Paul parish in Boonville were able to fill the gap in priestly duties at St. Joseph until May of 1979. It was during this time that Bishop Michael McAuliffe, of the Diocese of Jefferson City established a Team Ministry of Sisters to help oversee the pastoral duties at St. Joseph, under the guidance of Fr. Richard Hunkins of St. Mary parish in Glasgow, MO.  On September 3, 1979, Fr. Richard Hunkins was installed as pastor, and Sr. Lucille Meissen, C.PP.S and Sr. Eula Linnebur C.S.J. were installed as pastoral associates.

In 1981, St. Joseph found growth and prosperity, the parish boasted 120 families, along with many local college students that helped support the church growth. It was also during this time that organizational groups, including the Knights of Columbus and the Parish Council were established. With the growth and generosity of the parishioners at St. Joseph, the church was able to purchase ground adjacent to the church. Under the guidance of Sister Dorothy Miller, OSB, as resident pastoral administrator, the Parish Council begun addressing the growing need of the parish and started the plans for the construction of a educational/activity building in 1988. After the approval from Bishop McAuliffe, at the Diocese of Jefferson City, plans were begun for the construction of the new church hall. Parishioner, Gus Vandecnocke, drew up building plans for the construction, and presented those plans to the Parish Council in January 1990.  The Council recommended the plans be distributed and bids collected.

On May 1990, that Bishop McAuliffe came to St. Joseph to confirm the building plans and speak with parishioners on the parish needs. Then in September of the same year, final copies of the building plans were presented to the Bishop and the parish asked for help in obtaining a grant from the Catholic Church Extension Society. The grant was approved on October 15, 1991 and a pledge drive was started to fund the rest of the cost of the construction.

Work began on July 28, 1992 to construct a 60 foot by 100 foot building, divided into eight classrooms, a kitchen, restrooms, and storage areas. In March of 1993, the annual pancake and sausage breakfast was held in the newly constructed parish hall.

By the grace of God, in July of 1996, St. Joseph once again had a resident priest, Fr. Richard Colbert, C.PP.S. Fr. Colbert was resident pastor from 1995 to 1999. Unfortunately in 2001, St. Joseph lost their resident priest, again due to the priest shortage. Since 2001, St. Joseph has been joined with Saints Peter and Paul in Boonville, MO, sharing priests and sacramental preparations.

It was in December of 2020, that St. Joseph was joined with St. Mary, in Glasgow, MO, under Bishop W. Shawn McKnight's 10 county realignment plan. St. Joseph's current pastor is Rev. Joshua Duncan and a complete list of pastors and bishops can be found below.