The golden history of St Sebastian's High School begins from the year 1919. Before the year 1919, there was a school named Pope Leo XIII A V School(Anglo-Vernacular school), which was unofficially functioning near the chapel of Our Lady of Miracle, Thoppumpady, about two furlong away from the present St Sebastian's school. Due to some inconveniences, teachers and well-wishers asked the permission of the Parish Priest of St Sebastian's to shift the school. Rev Fr Francis D'Cruz allowed to restart the school in the corridor of St Sebastian's church with the new name St Sebastian's school, Palluruthy. Mr K.J. Joseph was the first headmaster of the school. The school is situated on the banks of Vembanad lake sandwiched between the old Mattanchery bridge and the new B.O.T bridge.

For the smooth functioning of the school, Rev Fr Raphael Edakkat took the initiative to construct a school building. In 1922 the school was recognized by the Education Department. This is the reason why the Jubilee is counted from 30th May 1922 onwards. Mr K P Antho was appointed as first headmaster of the newly recognized school.

In the year 1923, almost all the works of the new school building were finished. The inauguration of the new school building was done on 20th October 1924, the birthday of Rev Fr Raphael Edakkat. In 1927 began the form IV (equal to VIII std of this era). In the year 1929 St Sebastian's school was upgraded to high school.

The school started to function well in all the levels, the strength of the students increased, and there was the great need to accommodate the students. Rt Rev John Martin Rebeiro, the Bishop of Cochin of the time, helped financially to buy the property near the church and John Edakattu Memorial hall was constructed for the school.

In the course of time, an Old Students' Association was formed and at the right side of the church a two storied building was constructed by them under the leadership of Kochunni Master, the president of the Old Students' Association of that time. In 1961 K K Vishwanadhan M L A, the former student of the school laid the foundation stone and the new building was inaugurated by the Home Minister P T Chacko, in the year 1962.

In 2000 the school was upgraded to Higher Secondary School. Now St Sebastian's school is a big tree with branches. Primary section, High school section and the Higher Secondary section functioning under three heads. Marching ahead on the road to success, St Sebastian's High school promises a bright future to society.