Air Force Military School, Jos started as a direct reporting unit to Headquarters  Nigerian Air Force. However, the administrative and operational control of the school was later transferred to Nigerian Air Force Training Command Kaduna in 1996. The School has a board of Governors (BOG) that meet from time to time to deliberate on issues affecting the school. The day to day administration of the school is handled by the Commandant who is head of the school.

  Furthermore, the organizational structure of the school is slightly different from the typical Nigerian Secondary School. Both the academic programme and military training are carefully and judiciously integrated. The administrative structure therefore is planned in such a manner that all the specialist areas in the School work in liaison with each other to achieve the set objectives of the school. The school is divided into four (4) major sub-units namely, School Headquarters, Academic Wing, Military Wing and Students’ Wing. The Academic and Military Wings handle the teaching the teaching of academic and military subjects respectively, while the Students’ Wing takes care of the general welfare of the JAM. The school Headquarters coordinate all the activities of the various wings. Furthermore, in order to ensure smooth operation of all the school programmes, the wings have relevant squadrons and Flights under them. The detailed organogram of the school structure is as shown below.