The NAF organizational concept has been fashioned to meet current requirements of the service and the defence needs of the country. Resulting from its experiences in roles played from the civil war to other missions within and outside the country, the NAF is presently structured along a service Headquarters, 7 principal staff branches, 4 operational commands and 4 Direct Reporting Units.

The size structure and organization of the Air Force depends on a careful analyses of the perceived threat which could be enduring or emerging in either or both external and internal environment. Prior to the present organizational structure, the NAF had undergone some re-organization over the years. The first was in 1970, immediately after the civil war. The aircraft inventories were then grouped into Air Defence and Air Transport Wing. In 1978, the Tactical and Training Commands were established, Logistics Command in 1979 and in 2011, the Mobility Command was also established. The present establishment lays more emphasis on general service planning, establishing a linkage between tasking of formation or units and resource allocation. It also considered the development of quality personnel, timely intelligence, quick reaction operational force and the survivability of all NAF air bases and assets.