The Department of Chemistry of Cotton College was among the first Departments of the College that started in the year 1901. Prof. Chunilal De was the first teacher of the Department who taught both Chemistry and Physics. The Department has been functioning from the original century-old building of Cotton College. In 2001, a new building, the Harish Chandra Goswami Bhawan, was constructed by the side of the old building.

The B.Sc. Honours Course in Chemistry was introduced in 1913 -14 under Calcutta University. The Post-Graduate Course in the Department under Gauhati University was started in 1974. The Laboratories of the Department were recognized by Gauhati University for carrying out Ph.D. research in 1998.