The school was started in 1903 bearing the name of historical figure Kunhali Marakkar who sacrificed his life in freedom fight. The history of Kunhali Marakkar High School started from there. It was the need of time to start a school in Kottakal, an educationally backward area. The school was upgraded to upper primary school in 1966 and in 1976 it was upgraded to high school, fulfilling the long cherished dream of Kottakal people.

Higher secondary school was started in the school in 2002 under unaided stream, without any financial assistance from the government. In the begining it was only Computer Science batch started functioning with a limited number of students. In 2005 Biology Science batch was started. Well equipped laboratories, strict discipline, coaching based on individual concentration, personality development, career guidence and counselling, special coaching for backward students, partcipation in co-curricular activities and healthy interaction with parents are the specialities of Kunhali Marakkar Higher Secondary School. The students who completed +2 course from this school are now doing their higher studies and some of them are working in and outside India. Moulding the students educationally and individually to a right citizen is our motive.