Bajaur agency is administered directly by the Federal Government, through the Governor of the Khyber Pukhtoonkhwa Province as its agent. The agency is further headed by the Political Agent, who is assisted by Assistant Political Agents.
Bajaur Agency comprises of two sub-divisions, namely: Khar sub-division and Nawagai sub-division. Each of the sub-divisions is administered by an Assistant Political Agent. The Khar sub-division has been further divided into three tehsils, while Nawagai sub-division consists of four tehsils. Each of the seven tehsils is headed by a Tehsildar.