The school was established by the Mar Thoma Church Educational Society (MTCES) on 6 June 1966.

The principals since then were Located on the outskirts of Thiruvananthapuram city, St. Thomas Schools at Mukkolakkal has a 32-acre campus.

The residential school includes a state-of-the-art Computer facility and Science labs for the students.

These personal pictures of the two teenagers were described by the school as "indecent, scandalous, highly objectionable lascivious material which appeals to prurient interest.

"[2] Student's parents approached the Childs Rights Commission and Kerala High Court to move against school's action.

The Kerala High Court deemed the action of the school management to be legal and rejected an interim order from the Child Rights Commission that suggested the students be allowed to attend classes.

[2] School's stand is that students of opposite sex are not allowed to hug or shake each other's hands to congratulate each other and any such behavior is an act of indiscipline.