Nagaon Government Boys Higher Secondary School is one of the oldest schools in Assam. Initially, it was established as a high school on 17th November, 1865 by the then British Government. It was the third high school established by the British in Assam. The first one was established in Guwahati in 1835 and the second one in Sivasagar in 1841.

The school was started at the present site in a plain thatched house with mud floor with 5 teachers and 23 students. Janmejoy Das was the first head master of the school. The construction of the present school building, as it stands now, was completed in 1906. Till then, there were many additions and changes in the building in course of time, but the basic structure of the building remained same.

Initially, the school was under jurisdiction of Calcutta University and in 1948, when Gauhati University was established, it came under Gauhati University. The school was converted to a Higher Secondary School on 1st April, 1959 and the designation of the head of the institution was changed from Head Master to Principal. The affiliation of the school went to Board of Secondary Education in 1962, when Government appointed the first Secretary of the Board of Secondary Education, Assam. Class XI and Class XII came under purview of the Higher Secondary Education Council and Class IV to Class X remained under the Secondary Education Board of Assam(SEBA). In 1983, Class IV was abolished and in 2012 Class V was abolished from the school as per Government education policy. Class IX and Class X are now known as secondary classes and Class XI and Class XII are known as Higher Secondary classes as before.