The 10-acre site on which St. Malachy Catholic School is situated was formerly owned by Arthur and Emma Bennett and was farmland used for mixed farming and raising hogs.
The Metropolitan Separate School Board (now the Toronto Catholic District School Board) purchased the site on July 8 , 1954 and construction of the school began during the summer of 1969. St. Malachy opened in September 1969, in portables at St. Martin de Porres School. It had eight teachers and 225 students. The school moved to its permanent site in March, 1979. Mrs. Mary Michell was the first principal of the school. It was she who was instrumental in establishing an Irish flavour to the school.