Almost out of nowhere, Perlis rose to prominence in the mid 2000's, in the early days of the Malaysia Super League era.
The team representing the smallest state in Malaysia had shown potential in the last year of the Premier 1 era, in the 2003 season, finishing third in the league campaign, reaching the semi-finals of the Malaysia Cup and the final of the FA Cup, but it all came together in 2004, the first year the Super League was contested.
Under former player Norizan Bakar who was more fondly known as 'Cikgu Jan', the Northern Lions again ended their league campaign in third place, a somewhat disappointing finish considering that the league was only contested by eight sides at the time, and crashed out of the FA Cup in the third round, but they would shine in the Malaysia Cup.