The College is headed by the Commandant of the rank of Major General from the Army. The College being an inter service training institute comes under the functional control of Armed Forces Division (AFD). The Commandant co-ordinates with Principal Staff Officer (PSO), AFD for training support. He is responsible to the Governing Body, which is headed by the Prime Minister of the country. Under the Commandant, there is a Deputy Commandant of the rank of Commodore/Air Commodore who is either from the Navy or the Air Force.
The College is organized into two branches, namely, Training and Administrative Branches. The Training Branch is headed by the Chief Instructor of the rank of Brigadier General and the Administrative Branch by the Colonel Administration. The Training Branch has four wings namely the Army Wing, the Naval Wing, the Air Wing and the Academic Wing. A Senior Instructor of the rank of Colonel or equivalent heads each of these wings.
The Colonel General Staff (Col GS), who comes under the Training Branch, plans, programmes and co-ordinates all the training activities of the College. Presently, there are 10 syndicates in the Army Wing, 3 syndicates in Naval and 3 syndicates in Air Wing. Each syndicate consists of 12-14 students.
The Academic Wing is responsible for liaison with the Bangladesh University of Professionals (BUP) for Masters of Science in Military Studies (MSc) Programme. The wing is also responsible for conducting certain important modules of the course like Research Paper, Command and Leadership, and Strategic Studies. It publishes college journals and magazines namely Torch, the annual magazine of the course; Mirpur papers, the highly professional journal that includes articles of national and international interest; and Mirpur Newsletter, the yearly newsletter.
The Directing Staffs (DS) of the College are a highly professional body. They are the ex-graduates of the College, and normally join the College as a faculty member after attending second Staff College abroad. They are of the rank of Lieutenant Colonel or equivalent.