Catholicism came to Hamilton permanently in 1891 when the Jesuit Priest, Fr Alexander Diomedi, visited and began holding services in the home of Willie & Rose Brennan at 205 S 3rd St in Hamilton. Fr Diomedi was soon able to secure the site for a new church from Marcus Daly, and in 1896, under the leadership of Fr J. Guidi and about $5000, St Francis of Assisi Church was built.
For the first 11 years, the Jesuit Priests from Missoula's St Francis Church were in charge of Hamilton's new Queen Anne-Cape Cod style church. Then, in the fall of 1908, Fr MJ Carr became the first diocesan priest in Hamilton. At this point, Bishop John P Carroll raised the status of St Francis of Assisi Church to a parish. During the first years of the church, there were 50 Catholic families on the books. By 1910, this number was reported to have grown to 80 families, leading to the construction of the parish rectory next door.