Chhetri started his football career playing for school teams and then for his local club, City Club. Since then, he has represented I-League clubs Mohun Bagan, East Bengal Club and JCT FC. At Mohun Bagan, he scored eight goals over three seasons where the club finished in the bottom half of the league table every time. The next three seasons were spent at JCT where he scored a total of twenty goals including twelve goals in a single season where JCT finished second in the league. This earned him the league's "Player of the Year" award. Afterwards he played for East Bengal and scored seven goals in a season where they finished sixth. For the 2009–10 season, he signed with Dempo SC on a two-year contract. Sunil had signed a three-year contract with Queen's Park Rangers in August 2009. But a work permit was rejected by the UK government.