No. 6 Squadron was formed at Mauripur in August, 1947 without any equipment or aircraft on its charge with Flt. Lt. M. J. Khan as Officer Commanding. There was a good deal of trouble in running the orderly room because of shortage of clerks, lack of office accommodation, absence of telephones and non-availability of motor transport. Air Vice Marshal Perry Keene, A.O.C.-in-C RPAF visited the squadron on 16th August, 1947 - two days after the Independence - and told the officers and then airmen that No. 6 Squadron would be the only transport squadron left in Pakistan after the withdrawal of RAF squadrons; as such a very important and difficult role was awaiting it. The first RPAF Dakota was flown on an air test with Flt. Lt. A. K. S. Ahmed at the controls on 22nd October, 1947. The squadron soon settled down to the urgent requirements of service and assumed its role of passenger flying, equipment transportation, and supply dropping. The aircraft used were Dakota, Bristol Freighter, Wayfarer, Tiger Moth and Auster. On 29th June, 1948 a detachment of the squadron presented a guard of honour at Mauripur to the Quaid-e-Azam Muhammad Ali Jinnah on his arrival from Quetta. A sad yet memorable day in the history of the squadron came on September 9, 1948 when three Dakota aircraft did the fly past at the Quaid-e-Azam's funeral ceremony.

In October 1948 the squadron moved to Peshawar. On 14th November, 1948, one Dakota engaged in supply dropping in the Northern Areas was attacked by two RIAF Tempests, but the pilot Flg. Off. Dogar (later awarded Sitara-i-Jurat) brought the aircraft safely back to the base against heavy odds. On 22nd February, 1949, a squadron Dakota performed the first landing at Gilgit; in the following month was made a landing at Skardu. In May, 1949, the squadron moved to Lahore where during the ravaging floods of September, 1950, it was called upon to fly continuously on reconnaissance, photo recce and supply dropping sorties.

The squadron moved to its permanent location at Chaklala and was fully operational on 20th September, 1959. It received the C-130 aircraft in March, 1963, and on 30th June, 1963, Bristol Freighters were struck off its strength. For the first time on 17th April, 1967 a formation of five C-130 aircraft was flown.

In the September 1965 war, the squadron carried out 265 operational sorties. Sqn. Ldr. A. Masood Khan and Flt. Lt. V. A. Abadi were awarded Sitara-i-Jurat and Warrant Officer Ashfaq and Flight Sergeant Hafeez were awarded Tamgha-i-Jurat. The December, 1971 war saw the squadron again in action. Nine tactical and a number of logistic missions were made against heavily defended targets, and considerable damage was inflicted on the enemy. Flt. Lt. Mir Alam Khan and A. Wajid Salim were awarded the operational gallantry awards of Sitara-i-Jurat.