St Margaret's School was established in 1926, with 18 pupils, in the manse of the Toorak Presbyterian Church. In 1927 St Margaret's School moved to Mayfield Avenue, Malvern, and in 1931 leased the former Governor's residence, Stonington. By the 1930s St Margaret's School had grown to 330 pupils.
In 1929 the Berwick Presbyterian Girls’ School (our current site) was purchased. This branch of the main School was established in 1930, with a purpose-built boarding house, Campbell House.
In 1941 the whole School was established at Berwick as a rural boarding school and ran as such until 1978. In 1947 the School was purchased by parents and Old Girls from Miss Gipson, who retired.
St Margaret’s School was incorporated in 1948 and the first Council established.
Miss Dora Gipson 1926-1947
Mrs Hilda Strugnell 1948
Miss Elizabeth Woodyatt 1949-1964
Miss Ruth McGuire 1964-1978
Mrs Joan Butler 1979-1986
Miss Virginia Henry 1987-2000
Dr Helen McDonald 2001-2011
Mrs Paula Anderson 2011-2012
Mr Doug Bailey 2012-2016
Ms Carole Reed 2016
Ms Annette Rome 2017 –