The Parish of Chiltern was created in 1876 and included Rutherglen.
Chiltern continued as the centre until 1923 when due to the death of the then Parish priest Father Dean Gaffey and economic changes in the district the focus of the Parish moved to Rutherglen.
It was in 1901 at the request of Father Michael O’Connor the parish priest from 1895-1905 that a group of Presentation sisters left the Star of the Sea, Elsternwick to open a new Convent in Chiltern and teach in the two schools of the Parish, Rutherglen & Chiltern.
St Joseph's Chiltern was opened on 8th March 1901 and the founding Sisters of the Presentation Order
In 1913 a new brick school was built beside the Catholic Church
In 1924 the Sisters moved into the vacated presbytery on the same site as the church and primary school.
During the years the numbers at the school have varied. As mining prospects decreased and mines closed numbers decreased however as post-mining pursuits of grazing, agriculture, vines and wine making expanded so did the school numbers.
The Presentation Sisters continued with their dedication of teaching the children of the area from 1901 until the 1970's.
In 1961 Chiltern once again became a parish in its own right and the convent reverted back to a presbytery. Therefore from 1961 the Chiltern Presentation Sisters moved to Rutherglen and drove back to Chiltern on a daily basis to fulfil their teaching commitments.
With the commencement of Commonwealth funding for Private Schools in the 1970's lay teaches were being employed. It was in 1973 the Presentation Sisters withdrew from Chiltern and in 1974 the first lay principal Miss Sue App was appointed. The Current Principal Mrs Jennifer Hogan who was appointed in 2018.
In 1984 major renovations and refurbishment of the school building were commenced. This included the addition of a classroom/multi-purpose room at the rear of the building. In 1998 to accommodate the increased numbers at St Joseph’s a portable classroom was situated on land at the rear of the school. It’s colour scheme was selected to reflect the heritage value of the school. November 2001 saw the completion of a walkway between the main building and the toilet block and the construction of a well needed storage shed which was positioned next to the portable classroom at the back of the school.