In 1988, this squadron was stationed at PAF Base Rafiqui, and was equipped with A-5 aircraft. The year was full of operational commitments. In addition to one Flat Out and two Wide Awake Exercises, the squadron carried out the Long Shadow Exercise in February, and Hit Hard-VI, VII and VIII in April, June, and August 1988, respectively. In addition, the Fake-XIV and Shako Exercises were also carried out. The squadron also participated in a Durandal bomb drop exercise at Sonmiani range in December. In the later half of the year, 1 vs. 1 DACT missions were carried out, evaluating the performance of the A-5 against the F-7P in close combat.

In 1989, apart from taking part in Hit Hard exercises, the squadron participated in the Armement Competition. During the Fire Power Demonstration that followed the competition, the squadron carried out level delivery of Mk-82 bombs. During the month of May, five more aircraft were added to the squadron's inventory. In November 1989, the squadron was deployed at PAF Base Farid for Exercise High Mark. At the end of the year, the Inter-Squadron Dive Bombing Competition was held between 16 and 26 Squadrons, which the 16 Squadron won.

During 1990, the squadron carried out one Flat Out and three Wide Awake exercises. Exercise Tondo-II, III, and IV were also carried out. In the middle of the year, the Officer Commanding, Wing Commander Zafar, went to China to carry out evaluation trials in A-5M and F aircraft. The squadron pilots also went to Sargodha to undergo SCUP.

During 1991, three FT-6 aircraft, fitted with Martin Baker seats, were added to the inventory of the squadron. In addition to the exercises Flat Out and Wide Awake, the squadron also participated in Exercise Combat-VI, Sore Eyes-III, and Condor-II. During November, the squadron moved to Multan and during its stay there, it flew 115 sorties with 100 per cent serviceability and reliability.

During 1992, the squadron carried out four Wide Awake and three Flat Out exercises. The squadron also participated in DACT Camp in April and May. In June, Exercise King Cobra was held in which the squadron achieved 100 per cent results. During 1993, in addition to the routine exercises, the squadron carried out DACT in month of May and participated in High Mark Exercise in October. During 1995, the squadron participated in the exercise Saffron Bandit followed by exercise High Mark.

In January 1996, the squadron proceeded to Masroor for air-to-air firing. During this year, three Wide Awake and three Flat Out exercises were also carried out. During 1997, the squadron participated in exercise Fire Fox in March. This was an Air Defence exercise aimed at generating low level tracks for interceptors.

The year 1997 was full of squadron movements. The squadron was deployed twice to Minhas for a DACT Camp, and to Murid and Minhas as the runway of its parent base was being re-carpeted. The squadron was also deployed at Chaklala for ADA duties. The last deployment was at Sargodha for participation in the exercise Saffron Bandit. The squadron also participated in the fly-past on 7 September in connection with Pakistan's Golden Jubilee celebrations. Besides, the squadron carried out routine Wide Awake and Flat Out exercises. In one of the Wide Awake exercise, the canopy of an A-5 aircraft blew-off in the air, while it was proceeding to the range. The aircraft landed safely at the home base. It was during this year that operations on the Jamurd Range were discontinued as it was handed over to civil authorities.

In April 1998, the squadron participated in exercise Zarb-e-Aahen and exhibited a high standard of professionalism that was appreciated by the Corps Commander who had witnessed the entire exercise. In appreciation of the performance of the squadron pilots, he visited the squadron along with AOC, NAC, Air Vice Marshal Pervaiz Mirza, and presented a memento to the squadron. The squadron was awarded the ACES Trophy for the best performance, from among all tactical attack squadrons, in the year 1997.