With the birth of Pakistan on 14th August 1947, No. 6 RPAF Squadron came into being although it had already existed for several years before independence as an RIAF unit. The squadron inherited 1 serviceable Dakota with 2 pilots, 3 navigators and 3 signalers stationed at Peshawar. To remedy this paucity of men and material, the RPAF drew up a three-phase program; in the first phase, ending on 31 March 1948, No. 6 Squadron received 7 more Dakotas and during the next twelve months the aircraft strength went up to about 20.

During this period a pattern of operations was established by the squadron for supply dropping in Azad Kashmir. These missions were essential for keeping troops and villages cut off by snowbound roads supplied with the essentials of life. Flying fully loaded Dakotas with an effective ceiling of not much above 10,000 ft, in an environment of peaks ranging from 16,000 to 20,000, No. 6 Squadron could accomplish these missions only by following the sinuous curves of the Indus valley. During November 1948 the squadron, operating from Risalpur and Peshawar, air dropped some 88,000 lbs. of supplies. On 4 November 1948, a Dakota piloted by Flying Officer Mukhtar Dogar was attacked by 2 IAF Tempests. The pilot skillfully evaded the attackers and brought the Dakota back to base. Flying Officer Dogar was awarded the Sitara-e-Juraat for this act of gallantry. He was the first officer of the squadron to receive a gallantry award.

In early 1950, a large number of Bristol Freighters was purchased from the UK and added to the fleet of No. 6 Squadron. Their performance was similar to that of the Dakotas so no new techniques were necessary for the conduct of Northern Area operations. The generous reserve of Bristol Freighters enabled No. 6 Squadron to undertake an extensive range of transport and communication tasks within and outside Pakistan for nearly fifteen years. In 1955, some of the aircraft were adapted to carry a 4,000-lb. 'block buster' bomb beneath each wing and the squadron carried out a limited amount of training for a night bombing role against lightly defended targets. This paved the way for similar operations at a later stage with its C-130s.

The squadron acquitted itself creditably during large scale food dropping missions in the 1952 floods; a Sanad to this effect was presented to the unit by the Governor of the Punjab on 17 August 1952. From 15 to 30 November 1953, operation 'Snow Drop' was carried out to deliver supplies in the Northern Area. Chaklala was used as a forward base and 800,000 lbs. of supplies were dropped in seven hundred and eighty hours of flying. In 1955 the squadron also demonstrated supply dropping during an air display witnessed by the Defence Minister General Muhammad Ayub Khan at Lahore.

During its formative years, 6 Squadron gained valuable operational experience on Bristol Freighters in a variety of climatic and geographical environments, ranging from the snowbound peaks of Kashmir to the desert of southern Punjab to the tropical forests of East Pakistan. In 1963, when 4 Lockheed C-130Bs were received under the US aid programme, it enabled the squadron to begin phasing out its Bristol Freighters. The Hercules also allowed the squadron to revise its valley flight procedures by over flying the Karakorams before letting down over the destination air strips and drop zones, with a corresponding improvement in safety margins.

During the 1965 war, the PAF offensive against bases included assaults by para commandos, who were dropped at night from 3 C-130Bs near Adampur, Halwara and Pathankot. In another role, the squadron was able to convert its Hercules aircraft into night bombers for raids against battlefield targets with up to 22,000 lbs. of HE bombs, which were rolled out of the rear ramp on pallets. The squadron flew over twenty such missions and dropped bombs on enemy forces moving up for the battles of Chawinda and Pulkanjari. Seven officers were awarded the Sitara-i-Juraat and 2 JCO's the Tamgha-i-Juraat.

After the 1965 war, 6 Squadron continued its task of logistic support for army units stationed in the Northern Areas and of routine PAF commitments in both wings of Pakistan. The squadron came under tremendous pressure towards the end of 1970 when the political situation in East Pakistan became unstable. The unit efficiently completed the task of moving a large number of troops from West to East Pakistan. In 1970 the squadron also participated in extensive flood relief operations in East Pakistan. When civil war erupted in East Pakistan in March 1971, 2 C-130s were permanently deployed at Dhaka; they remained there till the December war broke out. These aircraft took extensive part in evacuation of troops and civilians from hostile areas. Wing Commander Munim A. Khan and his crew lifted a record figure of 365 people from Sylhet to Dhaka in one C-130 sortie. During 1971, the Indian government had stopped PAF flights over India and the squadron's C-130s proceeding to East Pakistan had to route via Sri Lanka, entailing sorties of exhausting length as well as the risk of interception by Indian fighter aircraft.

When war broke out on 3 December 1971, the squadron undertook tactical bombing raids in West Pakistan in much the same way as it had done in the 1965 war. A C-130 captained by Group Captain Mir Alam made a very successful attack against Jaisalmer and inflicted heavy damage upon the IAF's technical complex there. The crew were awarded Sitara-i-Juraat for this action. Successful bombing was also carried out in the Srinagar valley and against battlefield targets. The squadron did not suffer any war loss of life or equipment.

The squadron regularly participated in CENTO exercises 'Nejat' and produced good results; the exercises were held at Masroor, Rezayiah (Iran), England and Turkey. Every year the squadron takes PAF Air War College for its educational tours abroad. Since 1971 the college teams have been taken to China, England, Australia, North Korea, Germany, Egypt, Syria, Cyprus, Singapore, Malaysia and Sri Lanka. Owing to its increased commitments, some additional C-130Es have been provided to the squadron during the last decade.