The administration of the school is vested with The Mar Thoma Church Educational Society, which is a premier educational agency registered in 1966 under the Travancore – Cochin Literary Scientific and Charitable Societies Registration Act, 1955.
The Society runs four other reputed institutions inside the campus (St.Thomas Nagar, Mukkolakkal,Tvpm) :–
- St. Thomas Residential School (ICSE)
- St. Thomas Higher Secondary School (S.S.L.C)
- St Thomas Training College
- St.Thomas Pre-Primary Education Centre.
The society also runs three other institutions outside the campus.
- St. Thomas Play School at Kumarapuram
- St.Thomas Public School (CBSE) , Mar Chrysostom campus, at Kattaikonam
- St.Thomas Institute of Science & Technology in the Mar Chrysostom campus, at Kattaikonam.
All the institutions are managed by the Executive Committee of the Society which is presided over by the Bishop of Trivandrum-Quilon Diocese of the Mar Thoma Church. The Metropolitan of the Church is the Patron of the Society. The Secretary of the Society is the Manager of the School.