Pakistan participated in the tournament for the first time in 1992, finishing fourth in their five-team group at Rajshahi Stadium in Bangladesh in May 1992.

In the 24th minute midfielder Mohammad Ayub scored for Pakistan until Maldives fought back and their striker Ahmad Saleh levelled the game.

Nepal's stopper back Gambir Rai scored the lone goal in the ninth minute from a penalty.

It finished fourth in its six-team group, securing wins against Maldives (4–0)[5] and Afghanistan (3–1), but losing against Kuwait (0–2), United Arab Emirates (0–2), and Yemen (0–4).

Pakistan participated in the inaugural SAFF U-16 Championship held in Kathmandu, Nepal in 2011 with Sajjad Mehmood as the head coach, Hassan Baloch as manager and Munir Aftab as the captain.

The team withdrew from the 2015 SAFF U-16 Championship due to conflicts among the government and the Pakistan Football Federation.

In July 2012, three under-16 players went to Abu Dhabi for a month-long training camp at the Manchester United Soccer Schools.