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, with a small number of day pupils. 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. In 1949, Miss Elizabeth Woodyatt became Headmistress. In 1953, the new Memorial Hall was completed. Records show 80 pupils were at the School.

In the 1960s, boys were enrolled, up to year 3, in recognition of the fact that many parents wanted a family atmosphere for their children's first years at school.

St Margaret's competed in the Girls' Schools Association competition against other non-denominational girls' schools until 1975. 1978 saw the closure of the boarding school and the successful transition to day school.

From 1979 a change has come with a greater focus on academic excellence, new facilities and curriculum development. St Margaret's School in Berwick has built on its strong heritage to provide our students with the skills and initiatives necessary to achieve at both local and global levels.