The School is affiliated to CBSE Board and the students are being prepared for the All India Secondary School Examination. The Syllabus is prescribed by the CBSE. The Medium of Instruction is English. The School conducts classes from L.K.G. to class XII.Subjects taught in Secondary Section are English, Hindi, Malayalam, Mathematics, Science, Social Studies, Computer, Physical and Health Education, Art Education, Work Experience, General Knowledge, and Moral Science.St. Thomas Public School Senior Secondary Section offers the following groups for Class XI in Science stream.

Group A English, Maths, Physics, Chemistry, Biology
Group BEnglish, Maths, Physics, Chemistry, Computer Science
Group CEnglish, Biology, Physics, Chemistry, Informatic Practices