​Aeronautical Science focuses on the world of aviation with the emphasis on the technological aspects of military aviation and not on the historical or strategic implications of air power itself. The aeronautical science modules have been developed with the needs of active aircrew in mind. The focus is on the principals and theories, which provide insight into aspects and issues of current and future importance, from a perspective of the safe, orderly and efficient conduct of aircraft flight operations. Aeronautical Science is, therefore, only available to South African Air Force (SAAF) pupil pilots and student navigators at a first year level and qualified SAAF pilots and navigators at a second and third year level.

The first year modules of Aeronautical Science have been developed to satisfy the needs of the South African Air Force by presenting the theoretical phase of the SAAF pilot / navigators course at the Military Academy as Aer Sc 1 (Basic Aviation Theory). This is done through a unique evaluation method where the mastery level required for the SAAF pilot / navigator course is adhered to within the pass requirements of the Stellenbosch University. The modules are presented through a system of self-paced, instructor-led and instructor-assisted methodology by utilizing computer-assisted education. The first year modules include Airmanship, Meteorology, Aerodynamics, General Navigation, Piston Engine and Gas Turbine Engine Theory, Instruments and Avionics.

The second and third years are presented as distance education modules where aircrews are equipped with the generic theoretical foundation required to be able to operate in a highly advanced air situation in the latest generation aircraft platforms. The various disciplines that affect the world of military aviation, i.e. electronic warfare, weapons systems and advanced avionics are integrated in the second and third year.