With a long history of more than 180 years, the Scottish Church Collegiate School owes its origin to the Scottish Church College, when in its centenary year the mother institution was bifurcated into School and College departments and the School section was named as the Scottish Church Collegiate School.

Alexander Duff, who arrived in Calcutta on 27 May 1830, as the first overseas missionary of the Church of Scotland to India, felt the urgent necessity to spread the light of systematic education among the young generation of the city. He also strongly felt that the English language should be used as the medium of instruction, as it was the key to Western knowledge. With the aim of teaching all kinds of secular subjects, alongside the Bible and with the active support of the elite Indians like Raja Ram Mohan Roy and others, he founded the General Assembly's Institution on 13 July 1830, in Feringhi Kamal Bose’s house, located in 51 Upper Chitpore Road, near Jorasanko. The school continued in the same building until 1836, when it shifted to the house of Gorachand Bysack at Garanhatta, where the Oriental Seminary now stands. Finally, it was transferred and settled in its newly constructed palatial building on the Cornwallis Street (now Bidhan Sarani) in 1910.

Meanwhile, 450 evangelical ministers of the Church of Scotland broke away from the parent body and formed the Free Church of Scotland, which is known in history as the Disruption of 1843. Consequently, Alexander Duff left the General Assembly’s Institution, as he sided with the Free Church and established another separate educational institution in Calcutta, named as the Free Church Institution, which commenced its work on 4 March 1843. However, the Free Church Institution and the General Assembly’s Institution, both founded by Duff, were merged together to form the Scottish Churches College in 1908. On a later date, it was renamed as the Scottish Church College, after the official union of the established Church of Scotland and the Free Church in 1929. Subsequently, in 1910, the school was finally transferred and settled in the newly erected building on the Cornwallis Street and was named as the Scottish Church Collegiate School.

Later, to accommodate the increasing number of students, another building was constructed by the side of the main building, which was actually, the playground of the School, situated on Roy Bagan Street. The building was further extended in 1958 and named as Hensman Block after the then headmaster JC Hensman.

The Scottish Church Collegiate School is officially under the Governing Body of Diocesan Schools, the Diocesan Board of Education and the Church of North India and is affiliated with the West Bengal Board of Secondary Education (WBBSE), and the West Bengal Council of Higher Secondary Education (WBCHSE) for the secondary and higher secondary school examinations respectively.