The Japan international beat off competition from Syria's Firas Al Khatib, Kengo Nakamura of Japan, Iranian Hadi Aghily and Sayed Mohamed Adnan of Bahrain at the ceremony held in Kuala Lumpur.
He won the award after receiving the most points in terms of MVP awards during the 2009 season, which covers AFC Champions League matches, AFC Asian Cup matches, FIFA World Cup qualifiers and other tournaments organised by AFC.
29-year old Endo, who made the top five last year but lost to Uzbekistan's Server Djeparov, said it was a great honour to win the award.
"I would like to thank the AFC for this Award," said Endo. "This is a big honour for me.
"I was here last year but unfortunately, I wasn't able to win. However, I am very happy to win this year.
"I hope I can be a role model for young players everywhere and give hope to others in Asian football."
Other AFC annual award winners for 2009 included:
Coach of the Year: Huh Jung-moo (KOR) Club of the Year: Pohang Steelers (KOR) National Team of the Year: North Korea Youth Player of the Year: Ki Sung-yeung (KOR)