The MBTA Police Department operates under the direction of Police Chief Paul MacMillan. Chief MacMillan oversees the management, planning and direction of the Police Department.

Organizationally, the MBTA Transit Police Department is made up of the following four divisions: Patrol Operations, Homeland Security & Emergency Preparedness, Investigative Services, and Administrative Services. A Deputy Chief manages each division.

Superintendent-in-Chief Joseph O′Connor oversees all daily operations of the Department. The Division Commanders and the Night Commander report directly to the Superintendent-in-Chief. He assists the Chief of Police with the overall management of the Department.

Deputy Chief Robert Lenehan is the Commander of the Patrol Operations Division. The Patrol Operations Division is responsible for the field operations of the Department including special events, special operations, and the honor guard function. The Patrol Operations Division consists of Police Officers and Supervisors assigned to staff the patrol beats of the Department.

Deputy Chief Kenneth Green oversees the day to day operations of the 3:30 pm and 11:30 pm shifts. He is also the Department's liasion to community partnerships. 

The Homeland Security and Emergency Preparedness Division is under the command of Deputy Chief Lewis Best. The Division includes the Intelligence Unit and works in collaboration with federal, state and local law enforcement agencies and other partners on homeland security initiatives. In addition the Division is responsible for emergency preparedness planning. 

The Investigative Services Division is under the direction of Deputy Chief John J. Mahoney III. The Investigative Services Division is responsible for investigating all crimes and serious accidents that occur on MBTA property and conveyances. This includes all MBTA buses, the subway system, commuter rail lines and commuter boats.

The Administrative Services Division, led by Deputy Chief Robert T. Fitzsimmons, is responsible for the Professional Standards, Planning and Research, Training and Court Case Management Units. The Administrative Services Division oversees the hiring and promotional process, career enhancement programs, and the MBTA Transit Police Academy. This Division is also responsible for investigating all citizen complaints and the administration of department property and equipment.