After the independence of India in 1947, the princely state of Cooch Behar was merged with India in 1950 as Cooch Behar district within West Bengal, and Jenkins School was declared as one of the state government schools. During that period many teachers joined the school under the patronage of the then king of Cooch Behar, Maharaja Jagaddipendra Narayan and the government of West Bengal. Between the late 1940s and the early 1960s, the school flourished under the leadership of headmaster Kalipada Mukherjee. The Maharaja also employed Sailen Datta, a veteran cricketer of the Bengal cricket team for the upliftment of sports education in the school.

The National Award for Teachers was given to Prabodh Chandra Goswami, a popular mathematics teacher in Jenkins School in 1958, the first year that the award was instituted.

The 100-year anniversary of Jenkins School was celebrated in January 1961. January 2011 saw the celebration of 150 years of the institution.

The first line of the school anthem is "Moder Jenkins School, Biharo Tirthe Amar-o Kirti, Banir Punnyo Deoul…."