Khyber Agency is administered directly by the Federal Government, through the Governor of the Khyber Pakhtunkhwa Province as its agent. The administrative head of the agency is the Political Agent, who is assisted by Assistant Political Agents. The PA operates from the agency headquarters in Peshawar.
The Agency has three sub-divisions; Landi Kotal, Jamrud and Bara, with three Assistant Political Agents, seven Tehsildars and a number of other administrative functionaries. The headquarters of the Political Agent is at Peshawar, but has also a Camp Office/Residence at Landi Kotal. The Assistant Political Agents have their headquarters in Landi Kotal, Jamrud and Bara, respectively.