Subsequently, he moved to JCT FC (then known as JCT Mills) for the 2005–06 season. That season, Chhetri scored two goals in all competitions, one against Salgaocar and the other against SC Goa, with JCT finishing sixth in the league. After his game against the Brazilian club São Paulo FC in the Super Soccer Series in 2007, comparisons were drawn with fellow Indian striker Baichung Bhutia. He also scored two hat-tricks for Delhi in the group stages of the 61st Santosh Trophy against Orissa and Railways. Delhi were eliminated in the pre-quarter-final playoffs, however, after losing 1–0 to Tamil Nadu in extra time.
"I have played so much in Delhi. It's a great feeling to be clubbed with some of the legends."
At the end of the 2006–07 season (the last NFL before it became the I-League), Chhetri was awarded the league's "Player of the Year" award as well as the best forward award. He scored a total of twelve goals in the league as JCT finished second behind Dempo SC. His twelve goals included two which came in a 2–0 win against Mohun Bagan and another double in a 3–2 win against Dempo SC. In the first I–League season, Chhetri scored seven goals as JCT finished in third place. That season, his solitary double was against Salgaocar in the last game of the season. He was selected as the AIFF Player of the Year 2007 for his excellent performances for his club and country. In October 2008 he sparked interest overseas from clubs Estoril Praia of the Portuguese second division, Liga de Honra, and Leeds United of the English League One. Although there had been no deal agreed with Leeds, Chhetri spoke in an interview saying, "Nothing has been confirmed as yet but yes, I think I am close to getting there," however a deal never materialised and he instead moved to East Bengal Club.