Chowdhury joined the erstwhile Civil Service of Pakistan (CSP) in 1971 and appointed to BCS (Foreign Service) in 1974.

After joining the service, he did training in Civil Service Academy in Lahore and Diplomatic Training in International Institute of Public Administration in Paris.

Chowdhury served in Bangladesh Missions in Geneva, Kathmandu, New York and New Delhi. He was also Ambassador to Turkey and Russian Federation.

He represented Bangladesh in various committees of the UN bodies and attended UNGA, UNCTAD, ITC, GATT, ILO, WHO, HRC as a member of Bangladesh delegation.