One of the SAAFs front-line squadrons for many years, 3 Squadron was formed in January 1939 at AFB Waterkloof equipped with the Hawker Hartbees and Hurricane Mk II. In September 1939 the squadron moved to Port Elizabeth before being disbanded, only to be reformed at Waterkloof once again on 9 September 1940 with Hurricane Mk 1s. By October the squadron was involved in fighting in East Africa. Flying both Hurricanes and Gladiator Mk IIs, the squadron fought all the way through Somaliland and Abasynia and by the end of 1941 had destroyed over 100 Italian aircraft (24 in air combat). After moving to Asmara, the squadron was disbanded. The squadron was reformed in December 1942 and sent to the Middle East. Flying fighter defence over the port of Aden with Hurricane 11c and Spitfire V aircraft, coastal patrols were also flown from North Africa. Re-equipped with Spitfire IXs in August 1944, 3 Squadron was sent to Italy. Most of its operations involved strafing sorties. Disbanding followed at the end of the Second War War.

Three Squadron was reformed at Baragwanath Airport on 6 September 1952 as a part-time citizen force unit flying Harvards, but disbanded once again in 1957.

In August 1966 the squadron was reformed at AFB Waterkloof as a unit under the control of 2 Squadron, equipped with some Mirage IIIEZs. In February 1970 the unit received squadron colours and in the same year, hardware in the form of the Mirage IIIDZ. The squadron was reactivated as an autonomous squadron in February 1975, receiving the Mirage F1CZ in April 1975 when its Mirage IIIEZ, DZ and D2Z aircraft were transferred to 85 Advanced Flying School. The squadron continued to operate the Mirage F1CZ from Waterkloof AFB with frequent deployments to Namibia during the Border War. Three Squadron was disbanded when the Mirage F1CZs were retired on 30 September 1992.