The school was founded in 1938 by the late Mr. William Thomas Keble M. A. (Oxon), whilst Sri Lanka was still under British colonial rule. The school was the first Preparatory School to be established in Sri Lanka based on the English Primary School model.
Mr. Keble, was an eminent British scholar, author and educationalist. He was also the first headmaster of this school. He was an alumnus of Keble College Oxford, which is named after his maternal granduncle John Keble. He was the author of two books 'Ceylon Beaten Track' and the novel on Sigiriya. He arrived in Ceylon (The name for Sri Lanka during the British colonial governance) in 1928 to join the staff of S. Thomas' College, Mt. Lavinia, during the tenure of Warden Kenneth McPherson.
The school was established during the episcopate of Rt. Rev. Dr. Mark Carpenter-Garnier M A. (Oxon) D. D. who was the 6th Bishop of the Diocese of Colombo, who rendered significant assistance to Mr. Keble, during the establishment of the institution.
The institution which commenced with a student population of 95 boys and a staff comprising of 7 teachers currently has a student population in excess of 900 and over 80 members of staff. Initially, the school only accepted students between the ages of 5 -11, as the founding fathers of the school sought to remedy a conceptual void in the educational system by placing a new emphasis on the requirements and aspirations of younger children to be educated and to be allowed to express their creative talents and faculties unfettered and unhampered by older and more mature students. Nevertheless, over the years the school commenced accepting and educating older students.

The school is governed by the Anglican Church of Ceylon. It is classified as a private fee levying school, and is not at all financially dependent on the government. It is administered by a Board of Governors (established to the S. Thomas' College Board of Governors Ordinance No.7 of 1930) of which the Chairman is the Bishop of Colombo, thereby retaining the connected between the Church and the School. The day-to-day activities of the school are taken care by the Headmaster. The school also has a Deputy Headmaster, and sectional heads for the Upper, Middle, and Lower schools.
The current Headmaster is Mr. N. Y. Casie Chetty.

The school year has three terms, each which is named after a period within the church. Lent Term - January to April Trinity Term - May to August Michaelmas Term - September to December

The current student population is in excess of 900 students, aged 5–16. The students are from multiple ethnic backgrounds (Sinhala, Tamil, Muslim and Moor). The four main faiths practiced by the students of the school, in descending order of frequency, are as follows, (Christianity, Buddhism, Hinduism, and Islam). The majority of students of the school live in the suburbs of Colombo and are from relatively affluent backgrounds.

The institution provides education exclusively in the Sinhala and Tamil languages up to the G.C.E. (Ordinary Level) in conformity with the educational policy of the State. The school teaches English as a second language. The main subjects to be taught at the school include English, Maths, Science, Sinhala and Tamil languages, Social Studies and History, Commerce, Electronics, Mechanical engineering, Health sciences and physical education. However, most administrative matters are conducted in English.

The school comprises of a great hall, over 50 class rooms, two chapels, faith rooms, two music rooms, two art rooms, two playing fields, cricket nets, a basketball court and cafeteria. The school further has separate laboratory facilities for science, electronics, and mechanical technology.

Students are allocated into four houses as follows; Abeynaike, Carpenter Garnier, De Saram and Keble. Abeynaike house is named after the first headmaster of S. Thomas' Preparatory School, Rt. Rev. Mark Rodolph Carpenter-Garnier is named after the Sixth Bishop of Colombo who was Bishop when S. Thomas' Preparatory School was founded, De Saram house is possibly named after Canon R. S. De Saram who was Warden of S. Thomas' College, Mount Lavinia when S. Thomas' Preparatory School was founded, and Keble house is named after the founder of S. Thomas' Preparatory School, Mr. W. T. Keble. The houses compete against each other in many sports events throughout the year. An athletics championship held annually in February allows students in each of the different houses to compete in numerous athletic events.

Mr. W. T. Keble (1938 - 1942) (Founder)
Mr. N. G. Abeynaike (1943 - 1950) (First Headmaster)
Mr. J. T. R. Perinpanayagam (June 1951 - August 1966)
Mr. J. S. L. Fernando (September 1966 - 1994)
Mr. N. Y. Casie Chetty (1995 - to-date)