Chaklala was already functioning as an RIAF station well before independence and a Para Training School (PTS) was located there. On 12 January 1947, a medical training centre under the command of Squadron Leader Haque was also established at Chaklala. On 14 August 1947, the PTS had the honour of presenting the guard at the lowering of the RIAF ensign for the last time when RPAF Station Chaklala was born. The base soon became the scene of intense air activity; in August alone, there were as many as three hundred and nine arrivals and departures in addition to frequent VIP movements. The station provided all ground handling facilities to Nos. 10 and 31 RAF Squadrons which conducted many Dakota flights for the evacuation of non-Muslims from various frontier regions and for air lifting migrants from India to Pakistan. Being located in a most attractive provincial On 20 September 1947, the Central Medical Board (CMB) was established at Chaklala under the command of Squadron Leader Mahmood . Like other RPAF stations, Chaklala was short of manpower and the departure of Indian and RAF units had given it a desolate appearance. Both runways had begun to sink and break up due to soil erosion and excessive traffic, and repairs could not be carried out for want of funds. Meteorological and fire services were almost non-existent and daily requirements were being met on, an ad hoc basis.

On 22 June 1948, a Bristol Freighter gave a demonstration of loading and unloading of equipment, which was perhaps the first indication of the station becoming a transport base. By October 1949, a detachment of 6 Squadron had been established at Chaklala, but the station's main role still related to the function of a forward repair and maintenance unit. No. 1 Air 0 P Flight and an air selection centre had also been established here.

On 1 January 1950, No 3 University Air Squadron of the Punjab was formed at Chaklala which, along with No. 1 AOP flight and the 6 Squadron detachment remained the three regular flying elements of the station till June 1954, when the Flying Instructors School (FIS) was established. At about this time No 3 Air Scouts Troop and No. 76 MODC Platoon were also raised at Chaklala. By January 1956, 4 additional units had come up at the base: No. 103 Air Logistic Depot, No. 2 Wireless Observer Squadron and No. 10 MODC Platoon were established here, while the Central Gliding School (CGS) was, moved up from Drigh Road to Chaklala.

The northern area air transport commitment had meanwhile grown from a single aircraft operation in 1949 to almost the full strength of a squadron, and from the mid-1950s onwards, transport squadron personnel were being continuously rotated at Chaklala from their parent station, Lahore. Finally in 1960 the entire air transport element of the PAF, i.e. Nos. 3, 6 and 12 Squadrons were moved to Chaklala, and since then the base has remained the hub of all peace time military air transport activity in Pakistan. In March 1963, the first four C-130s were received by No. 6 Squadron and on 29 June the C-in-C PAF flew in one of them for the first time. Next day, the Bristol freighters were struck off from the squadron establishment. Over two years later, in September 1965, the technicians and engineers of PAF Chaklala accomplished the unusual feat of making 4 phased out Freighters serviceable for war operations within just two days. During the war the base carried out 297 sorties against the enemy and 5 officers were awarded Sitara-e-Juraat. On 17 April 1967 a formation of 5 C-130s flew for the first time in an air display held at Chaklala. In 1971, the base had again become a centre of hectic air transport activity much before the war itself, because of the floods and civil disturbances in East Pakistan.

The base continues its function as a military air transport and VIP movement centre. It has had the privilege of accommodating the main component of Air Headquarters in its modern Transport Conversion School building since the early-1980s and boasts of providing functional or administrative support to more than 50 units today.