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In 1842, Maria Dyer, a British missionary with the London Missionary Society, started a school in a rented shop-house in North Bridge Road. It was a boarding school which gave orphan girls an opportunity to be educated for free. This was the first girls' school in Singapore and remained so for many years.
After the death of her husband Samuel Dyer, she had to return to Penang (she died a few years later in 1846) but the school continued. The first principal was Miss Grant. When another missionary, Sophia Cooke arrived from England in 1853, she took charge of the school. There were 20 pupils then. One of the first things that Miss Cooke did was to learn Malay, and for the next 42 years she devoted all her efforts and time to the school, giving her best to raising the level of education of the girls in the school. The school came to be known as the "Chinese Girls' School" (CGS), also "Miss Cooke's School".
There were lessons in scripture and great emphasis was placed on providing a Christian education. From an early age, the girls learned the meaning of Christian service. In the 1860s, two day schools were started for women and children. One was run entirely by girls from CGS and the other was held in the home of a former pupil. The school was so recognized for developing young women of good character and virtue that CGS was reputed the “training home for Christian wives”. Miss Cooke, who also started the YWCA movement in Singapore, was a devoted and fervent Christian. She was succeeded by Miss Gage Brown, the new principal.
CGS moved to 134 Sophia Road, opposite Government House in 1861. The Church of England Zenana Missionary Society took over the management of the school in 1900. 49 years later, it was re-named St Margaret’s School. The school became a grant-in-aid school in 1939.
The late Miss Jessie Kilgour was principal from 1938 to 1948. After the Second World War, the school was named St Margaret's School (after Queen Margaret of Scotland) by the late Bishop Wilson.
Miss Norah Inge became principal in 1948. Domestic Science became part of the school curriculum, a netball team was formed and a Girl Guide company was incorporated. It was Inge who first conceived the idea of building a separate secondary school.
1957 saw the late Mrs. Martha Holloway as the new principal and after much planning and hard work, the secondary school was built in Farrer Road. The Secondary and Primary Schools were separated in 1960. Holloway became principal of the secondary school and Mrs. Gertrude Song, principal of the Primary School.
In March 1966, Mrs. Mary Cassim was appointed principal of St Margaret's Primary School and July 1967, Mrs. Liza M George was appointed principal of St Margaret's Secondary School.
The building at 134 Sophia Road which continued to house the Primary School was demolished in August 1984. In its place was a new up-to-date and larger school, built to house future generations of St Margaret's Primary School girls.
The school occupied a holding school in Anthony Road while awaiting the completion of the new building. The shift back to the old site came in June 1986, with a new address -- 99 Wilkie Road. The new building was officially opened by the MP for Ulu Pandan, Dr Dixie Tan on St Margaret's Day, 16 November 1987.
Miss May Chew, who was vice principal from 1985, was made principal in January 1988. After her retirement in December 2003, Mrs Elsie Poey was appointed as the new principal.
Today, St Margaret’s carries on the work of Miss Cooke in preparing young women in the virtues of charity, patience and devotion.