One of the largest organizations in the country, the Pakistan Railways is Federal Government Department under Ministry of Railways. The Secretary for Ministry of Railways is also the Chairman of the Railway Board.

Pakistan Railways comprises of two functional units. The Operations Unit and the Manufacturing and Services Unit, each headed by a General Manager who is responsible to the Secretary / Chairman Railways for the performance of his Unit.

The Operations unit, with its Headquarters housed in the historic North Western Railway Headquarters building, an imposing landmark of Colonial-era architecture of Lahore, overseas train operations and all related functions. Three Additional General Managers, each heads of various specialized departments assist the General Manager / Operations in managing the operations unit. The Manufacturing and Service (M&S) unit is responsible for the management of the Concrete Sleeper Factories, Locomotive  and Carriage Factories, Workshops, Hospitals, Schools and two Consultancy firms, PRACS and RAILCOP.

Pakistan Railway Comprises of seven territorial operating Divisions i.e. Peshawar, Rawalpindi, Sukkur, Karachi, Quetta and Mechanical Division i.e., the Workshops Division at Moghalpura, and an administrative Division, the Headquarters. The territorial and Workshops Divisions are each headed by Divisional Superintendent reporting to General Manager / Operations. The Divisional superintendent is assisted by the Divisional and Assistant Officers of their respective department i.e., the Engineering Department Civil, Mechanical, Electrical, Signal and Telecommunications and the Medical, Transportations and Commercial, Accounts and Railway Police.