St Mary's School is an integrated Catholic Primary School of the Dunedin Diocese and is one of the earliest to be established being staffed by lay teachers.
In June 1873, Bishop Patrick Moran, the first Bishop of Dunedin visited Milton and before returning, examined the 42 children attending the School in catechism, reading, writing, tables and spelling. He had expressed to the people, his anxiety that they be provided with an efficient Catholic School and to help them, he advanced a loan to clear the remaining debt on the Church.
In January 1891, a Dominican Sisters Convent was established in Milton and Bishop Moran stated that the nuns had come to give the children a "real education - not a half education - not mere instruction, but an education that would develop all their powers of mind and body, that would develop all their religious instincts and moral principles, and an education that would prepare them for their several vocations hereafter in life…"
When the Dominican sisters took over the running of the school in 1891, the roll stood at approximately 120 pupils with children coming from as far away as Balclutha, Waihola, Allanton, Henley and Otakia.
In 1951, the present school was built. It was integrated into the state system in accordance with the 1975 Conditional Integration Act at the beginning of 1981 and it was at this time, that the Administration Block was added to the existing building.
In 2000, the School was redeveloped and underwent a major upgrade. This included the addition of an Office and Administration area. It also included revamp of all classrooms.
In 2005, due to a steady increase in roll numbers, the roll ceiling was lifted by the Ministry of Education.
In 2007, two additional classrooms and a resource room were added. A large asphalted area and a large tiled area were also added.
In 2012, the classrooms in the main block were renovated.
In 2019, parts of the school were re-clad in cedar and there was major maintenance done on the school building.