Due to the poor economic situation and Western arms embargos, the condition of the PAF F-104-fleet by the early 1970s was so poor, that most of the aircraft were non-operational and the sole unit that flew the type, No.9 Squadron, was provided with old F-86Fs to keep pilot hours up. The situation improved significantly in March 1971, when the USA channeled a shipment of spares to Pakistan, enabling the PAF to make the remaining five F-104A and two F-104B operational again.

No 9 Squadron moved to Masroor AB from Sargodha AB on 6 December with a total of 7 F-104 (5 F-104A, 2 F-104B).
Commanding Officer was W/C Arif Iqbal.
Another two (plus a RJAF F-104A) were lost to Indian AAA fire and MiGs respectively in the 1971 conflict.
Today six of the original fourteen are known to be preserved at various locations in Pakistan.

Only three of the aircraft has a combat history as far as we know.
- 56-0874 preserved at Peshawar had a Canberra night kill in the 1965 war and strafed a HF-24 on the ground at Uttarlai in the 1971 operations.
- 56-0879 preserved at Masroor shot down a Indian Su-7 Fitter on December 4, 1971 over Amritsar.
- 56-0804 shot down a Indian Folland Gnat F.1 on December 4, 1971 over Amritsar.

At PAF's request, all its F-104As were refitted with the M-61 20 mm Gatling gun, whereas its counterparts in the USAF had been divested of their guns on the assumption that all post-Korea air combat would occur at high speeds where only the wing tip-mounted Sidewinder missiles would be effective.
The PAF's foresight was amply rewarded in actual combat and the USAF too reverted to having machine guns as mandatory equipment on all its fighters in due course. The newer GE J-79-11A engine was also installed on the aircraft. The F-104A was able to carry AIM-9B Sidewinder air-to-air missiles on the wing tips and later (1971) as well on the underwing pylons. This made the Pakistan F-104s somewhat unique:
They had the gun and being the lightest of the F-104 series with a more advanced J-79 engine enjoyed the best thrust-to-weight ratio.
A retractable hook was fitted beneath the rear fuselage to engage emergency runway arrestor wires.

The US Government imposed an embargo on arms sales to both India and Pakistan as soon as the 1965 war began.
No consideration was given to the fact that India, a long-time ally of the Soviet Union, hardly used any American military equipment
and the sanctions exclusively degraded the combat potential of only the Pakistani Armed Forces.

The PAF fleet of F-104 was particularly hard hit by the arms embargoes. Eventually it became impossible to maintain a reasonable in-commission rate on the F-104s and the PAF decided to phase it out of service in late 1972. This ended the era of Pakistan Air Force's first Mach 2 combat aircraft.

Today six of the original fourteen are known to be preserved at various locations in Pakistan.
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note:
Royal Jordanian Air Force assistance during the 1971 war:
Nine F-104As of the RJAF arrived at Masroor (Mauripur) Air Base on December 13, 1971. The Jordanian pilots who ferried them were all operational pilots and they flew many air defense missions on these fighters within the Pakistani air space. The PAF did not allow them to fly cross-border offensive missions over the Indian territory.
Royal Jordanian AF F-104A in Pakistan: 56-767, 56-774, 56-775, 56-777, 56-789, 56-799, 56-839, 56-843, 56-845.
The Royal Jordanian AF aircraft were painted with PAF roundels during the 71 war. Usman Shabbir, November 20, 2007
The Pakistan AF lost three F-104 during the 1971 war including a RJAF F-104A with tail number 56-767 on December 17, 1971.
(F/L Samad Changezi was shot down (KIA) by F/L Aruna K. Datta flying a MiG-21FL). Usman Shabbir, November 14, 2007

F/L Amjad Hussain shot down a Mystere, 56-877 on September 7, 1965
Recent research conducted by Air Cdre Kaiser Tufail, which involved interviewing multiple witnesses, confirmed that Amjad indeed had a mid-air collision with the Mystere and was not shot down.