Established in 1789, St Thomas’ School located in Khidderpore area is the oldest school in the city, which owes its origin to the Charity School, founded somewhat between 1726 and 1731. According to the records preserved from 1787, the running of both the Charity Fund and the School were subsequently taken over by the St John’s Church. The proposal for establishing a Free School Society for the Education of the needy Children was submitted at a meeting held at the Old Court House on 21 December 1787, presided over by Lord Cornwallis, the then Governor of the Bengal Presidency. Thereafter, a general meeting was called on 21 April 1800, to unite the Old Charity School Fund and the Free School Funds.

In the mean time, the Free School started to operate on a site in Dalhousie Square, where the Scottish Church, known as the St Andrew’s Church stands today, adjacent to the Writer’s Buildings. Later, that site was sold and the school moved to an area near Park Street, after purchasing a building, built on a huge 15 bigha plot of land (24320.16 sq m), in 1790. Subsequently, the relative road, on which the building stood, was named after school as Free School Street. Today, part of that particular plot of land houses the food and rationing offices, the Free School Street Post Office and other buildings. However, a part of the St Thomas’ School still operates at the same site and is called St Thomas Day School, as legally it is a branch of the main St Thomas’ School.

At the beginning of the 20th Century, the authority of the School felt that the School premises on Free School Street was unsuitable and thought of shifting the school to Ranchi. However, the idea was abandoned as the parents vehemently objected. Next, their choice fell on the spacious Khidderpore House, situated at 4 Diamond Harbour Road. Accordingly, the Free School Society approached the government with their proposal in 1914, which was sanctioned and the extensive housing property was handed over to the Society in 1915.

While the School started in full form 1916 from the coveted premises, the school on Free School Street remained operating as the St Thomas Day School, a branch of the main school. In 1916, the name of the School was changed to St Thomas School Society. However, after the Legislative Council of Bengal passed the St Thomas’ School Act in 1923, the name of the School was finally changed to St Thomas’ School.

During World War II, the doors of the School were shut down for the students, as the Khidderpore House was converted into a military Hospital and the Boys section was shifted to Takdah, a quiet village near Darjeeling. However, when the War was coming to an end, it was shifted back to its own premises.

To meet the need of the day, new blocks gradually started to come inside the spacious compound of the School. While the Hospital Block was constructed in 1915, the present Girls’ School building came up in 1948. St Thomas’ School is the first Anglo Indian School in Calcutta, where the multipurpose higher education system was introduced in 1956. Consequently, the Boys’ School Science and the old Technical Block were constructed, a year later, followed by the Girls’ dormitory.

While the Jeanne D’Abreau Block was built in 1977, the John Siromoni Technical Block came up in the early 1980’s, on the site of the original Khidderpore House. The huge campus of the School, considered as one of the largest campus areas in the city, also houses the St Thomas' College of Engineering and Technology. St. Stephen’s Church, located on 3 Diamond Harbour Road, is right next to the St. Thomas Boys’ School. The school has adjacent division St. Thomas' Boys' School (STBS) and the students of this school feel proud to be known as the Thomasites (boys).

Equipped with three football size fields, two basketball courts and children's playgrounds, St Thomas’ School, a heritage institution of the city, guides students from kindergarten to class XII. According to the syllabus of the Council for the Indian School Certificate Examinations, the school prepares students for the Indian certificate of secondary education (ICSE) examination (class X) and the Indian School Certificate (ISC) examination (class XII).