Soon after independence, a signals and radar school was established in 1948 on the premises of an abandoned WW II airfield on the outskirts of Karachi, called Malir after a neighboring village. The school was to train all future radio and radar technicians of the PAF. The instructional staff was provided by a British company, International Air Radio Ltd (IAL). In 1949 PAF Malir was raised to station status, Squadron Leader A Salaam Butt being the first station commander. Offices of the station headquarters were housed in the building now occupied by PAF Model School.

The initial role of the station was to exercise administrative and supervisory control over the training activities of the Signals and Radar School, which was later to be called School of Electronics (SOE). The following year, a maintenance depot was also raised at the base with its administrative control vested in the station commander. A facility to train signals officers at Malir was added in 1957, and Pakistani officers and SNCOs took over the entire training task of the school from the IAL staff in 1959. In 1963 the SOE moved out to nearby Korangi Creek air base to join its sister institution the School of Aeronautics.

Immediately after 1965, a ground combater wing was established and placed under the administrative control of PAF Station Malir; in subsequent years 8 new units were located there. The present role of the base is to keep all its lodger units in a high state of preparedness for their wartime roles. During both the 1965 and 1971 wars, the air base fully met or exceeded its assigned commitments, and supported its field units by efficiently organizing several logistic points throughout the country.

The first Aero-modeling club in the PAF was established by Flight Lieutenant S R H Naqvi at the Signals and Radar School in 1953. The club was inaugurated by Air Vice Marshal L W Cannon, the C-in-C PAF.

From the early-1970s to date, the base has assumed additional responsibilities for training and maintaining the PAF's mobile elements in a high state of readiness. The base has grown substantially during recent years and the small village of Malir is now a fast expanding township.