[2] Khan Research Laboratories entered the National Football Championship in the 1998 season, where they lost 2–0 to Allied Bank in the quarter-finals.

[4] In the 2000 season, Khan Research Laboratories reached the Round of 16, when they topped the group again after defeating Punjab Greens and WAPDA 8–1 and 3–0, respectively.

Khan Research Laboratories defeated Federally Administered Tribal Areas 2–1 in the quarter-finals and lost to Pakistan Army 1–0 in the semi-finals.

[13] Khan Research Laboratories completed the double, when they won the 2009 National Football Challenge Cup defeating Pakistan Airlines 1–0 in the finals.

In the 2011–12 and 2012–13 season, Khan Research Laboratories completed a consecutive double when they won the League and Challenge Cup.

In latter seasons, they won the league after their star forward Kaleemullah Khan scored 35 goals including 7 hat-tricks.

In the 2014–15 season, they finished sixth after losing their star players, Kaleemullah Khan and Muhammad Adil to Kyrgyz club FC Dordoi Bishkek.

Khan Research Laboratories' first appearance in the Asian competition came in the 2010 AFC President's Cup, when they finished second to Vakhsh Qurghonteppa in the group stage.

Following the domestic football revamp in the country in 2023, departmental clubs including Khan Research Laboratories remained competing in the PFF National Challenge Cup.