Chhetri began his professional career at Mohun Bagan in 2002,[10][11] moving to JCT where he scored 21 goals in 48 games.[12] Sunil was part of Delhi team in the 59th edition of Santosh trophy held at Delhi. He scored 6 goals in that tournament including a hat-trick against Gujarat. Delhi lost to Kerala in the quarter finals and he scored in that match too.[13] He signed for Major League Soccer side the Kansas City Wizards in 2010, becoming the third player from the subcontinent of note to go abroad.[14] He returned to India's I-League where he played for Chirag United and Mohun Bagan before going back abroad, at Sporting CP of the Primeira Liga, where he played for the club's reserve side.[15]

Chhetri helped India win the 2007, 2009, and 2012 Nehru Cup, as well as the 2011, 2015, and 2021 SAFF Championship. He has also helped India win the 2008 AFC Challenge Cup, which qualified them to their first AFC Asian Cup in 27 years,[16] scoring twice in the final tournament in 2011.[17] Chhetri has also been named AIFF Player of the Year a record seven times in 2007, 2011, 2013, 2014, 2017, 2018–19 and 2021-22.[18][19]

Chhetri received the Arjuna Award in 2011 for his outstanding sporting achievement, the Padma Shri award in 2019, India's fourth highest civilian award. In 2021, he received the Khel Ratna Award, India's highest sporting honour and became the first footballer to receive the award.[20]