The announcement was made by AIFF president Praful Patel. Chhetri was chosen the winner after voting by Airtel I-League coaches.
Chhetri will be presented a prize of Rs.2 lakh besides a trophy.
The Indian captain, presently India's highest-ever goal-scorer in international football on 43 goals had earlier won the award twice, in 2007 and then in 2011. In the process he joins IM Vijayan to have won the award thrice each.
Oinam Bembem Devi was adjudged the 2013 AIFF Women's Player of the Year. Bembem Devi was the only recipient of the award the sole time it was announced in 2001.
The 33-year-old Bembem Devi will be presented a prize of Rs.1 lakh and a trophy.
AIFF also declared Jeje Lalpekhlua as the 2013 Emerging Player of the Year. The 22-year striker from Mizoram has already donned the national jersey 43 times scoring 14 goals so far.
All the Awards would be presented in an awards night in February organised by FICCI.