As the skirmishes between India and Pakistan started in the volatile region of Rann of Kutch, a flight of No 9 squadron under the command of Sqn Ldr Middle coat was dispatched to Mauripur. Farooq was also the member of this select group. The flight was tasked in the battle of Biar Bet to keep the Indian army away from Pak troops in the Kutch area. He flew numerous daring missions during this period and kept Indian army under pressure. Soon the dispute settled in favour of Pakistan. However the tensions started to build up in Kashmir. Anticipating an all-out war with India his flight was called back to Sargodha in August 1965.
As the war started in first week of September, he was detailed to fly the important combat air patrol missions over Kashmir. On 1 September, when Rafiqui drew the first blood in Chamb sector, he along with others provided the top cover to his formation. Throughout the 1965 war, the F-104’s played the role of bouncers, scaring away the IAF from attacking Pakistani troops.
The deterrence so created remained intact until the ceasefire. Farooq flew numerous CAP missions in Akhnur, Chamb, Wagah, Jammu and Samba sectors and provided shield to the various strike formations. In order to clear their tails and to make them successful.
Perhaps the most important event which shot him to sudden fame during the war was the ‘super sonic boom’ mission carried out at Amritsar. AM Nur Khan, being the visionary C-in-C asked him to perform a low level super sonic boom at Amritsar. The idea was to harass the enemy in the opening round of the war and also to prove the lethality of F-104 aircraft. He succeeded in both. On that fateful day, he flew two supersonic passes over Amritsar. During the first pass the ack ack opened up but it was no match to the super sonic flight of the Star (Link will despatch)Fighter. Immediately after the 1st pass he was asked to repeat the heorics for one more time.but This time the Indian guns were ready and they had providedan umbrella of ack ack fire , the sky was red and there was no way that any air craft can get through yet Farooq Umar was not deterred and he went through the mountain of the ack ack fire for 2nd time . By the time he landed back, All India Radio came up with interesting stories. It narrated that 8 F-86 aircraft attacked and had rocketed/bombed the Amritsar airfield. The mission thus succeded in achieving desired results.
Farooq also flew numerous Photo recce missions deep inside enemy territory. These daring missions provided valuable intelligence to PAF in making future moves during the war. In all he flew 23 combat missions during the war. He also played a key role in providing top cover in the battle of Chawinda, and Indian air force attack on Sargodha during which MM Alam shot down five Hunters, destruction of Amritsar radar etc.
After the 1965, war PAF leadership shortlisted French Mirage aircraft for induction in to the fleet of PAF. Not surprisingly, Farooq Omer was selected by MM Alam to be amongst the pioneering 6 pilots selected to lay their hands on the new weapon system and to become instructor pilots . He was also among the first badge of pilots who were selected to ferry 1st 6 Mirages from France to Pakistan via Italy , Turkey and Iran.