No. 5 RPAF Squadron was formed with 8 Tempest Mk II aircraft on 15 August 1947 at Peshawar under the command of Squadron Leader Zaheer Ahmad; most of its personnel came from No. 1 RIAF Squadron. Despite a shortage of technical manpower, the unit ably carried out its assigned task of watch and ward duties from Miranshah during the early period of its history. In December 47, the squadron took part in operation 'Curzon' during which it provided cover to the army which was being pulled out of Razmak.

The squadron was visited by the Prime Minister of Pakistan Mr. Liaquat Ali Khan in January 1948. He was accompanied by the RPAF C-in-C, Air Vice Marshal Perry-Keene and Air Commodore M K Janjua. On 11 April 1948, the squadron presented a smartly turned out guard of honour to the visiting Governor-General, Quaid-i-Azam Mohammad Ali Jinnah at Peshawar and two days later the squadron pilots participated in a fly past in the honour of the Quaid's visit to Risalpur.

In the early-1950s the squadron was reequipped with the Hawker Fury which was the best piston-engine fighter-bomber of its time. In June 1951 the squadron lost Pilot Officer I A Rafiqui in an air crash near Lahore. He was the elder brother of Squadron Leader Sarfraz A Rafiqui, H.J., who joined the same squadron as a pilot officer on 4 November 1953 and later commanded the unit from March 1963 onwards. In November 1951 Squadron Leader F S Hussain took over as squadron commander and a few months later the squadron won the inter-squadron armament trophy which he received from the C-in-C, Air Vice Marshal L W Cannon, on 12 February 1952.

On 1 September 1965, even before full scale war had started, 5 Squadron had the distinction of shooting down 4 IAF Vampires in the very first air engagement of that day. During the 1965 war the squadron flew one hundred and ninety hours in various types of operations. Squadron Leader S A Rafiqui shot down 2 Vampires and 1 Hunter aircraft. He was reported missing at 1800 hours on 6 September 1965, and later confirmed as killed in an engagement near an enemy air base. Flight Lieutenant Yunus Hussain, his wingman, also gave his life for the nation in the same action, after having shot down 1 Hunter. Flight Lieutenant Cecil Chaudhry of the same squadron accounted for 2 Hunters and 1 Canberra during the war while Flight Lieutenant A H Malik shot down 1 Mystere.

In 1967 the squadron was reequipped with Mirage-III E aircraft and assigned a tactical attack role in which the squadron had become fully operational before the 1971 war with India. During this war it flew over 200 day and night sorties which included counter air, photo recce and interdiction missions as well as air defence. The squadron participated in the first strikes against the IAF bases at Pathankot and Awantipura. It did not sustain a single loss throughout the war. Flight Lieutenant Naeem Atta shot down 1 Canberra aircraft at night and Flight Lieutenant Riaz Sheikh damaged 1 Su-7 aircraft. Wing Commander Hakimullah and Squadron Leader Farooq Omer were awarded the Sitara-e-Juraat.