Pakistan Navy won their first silverware in 2008, winning the 2008 National Football Challenge Cup, defeating Khan Research Laboratories 3–1 in the final.

They reached the finals of 2010 National Football Challenge Cup, where they lost 4–0 to defending champions Khan Research Laboratories.

In 2011–12 season, the club reached the semi-finals of 2012 KPT Challenge Cup, where they once again lost 1–0 to Khan Research Laboratories.

Pakistan Navy were the joint-highest placed team in the relegation zone with Habib Bank, sharing 35 points each.

In the second phase, they again topped their group after defeating Pakistan Television and Sui Southern Gas 5–0 and 1–0 respectively.

Pakistan Navy participated in the 2018 National Challenge Cup, reaching quarter-finals where they lost 2–0 to WAPDA.

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