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 Police Department is made up of the following three divisions: Patrol Operations, Investigative Services, and Administrative Services. A Deputy Chief manages each division.

The Patrol Operations Division, directed by Deputy Chief Joseph O'Connor, is responsible for the uniformed field operations of the department. Specifically, the Patrol Operations Division consists of day and night patrol units, motorcycle patrols, canine officers, the explosive detection unit, special operations, and community services.

The Investigative Services Division, directed by Deputy Chief Lewis Best, is responsible for ensuring the efficient management and performance of the Criminal Investigations Unit, Intelligence Unit, Anti-Corruption Unit and Crime Scene Services Unit. These units work to investigate and prosecute criminal offenders. Additionally, the Investigative Services Division oversees juvenile services, revenue security, civil rights investigations and accident reconstruction.

The Administrative Services Division, led by Deputy Chief Donald O'Connor, 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.