Endo, of J.League side Gamba Osaka, received 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.
Also nominated were Syria's Firas Al Khatib, Kengo Nakamura of Japan, Iranian Hadi Aghily and Sayed Mohamed Adnan of Bahrain.
The AFC Player of the Year Award is decided by MVP points awarded by Match Commissioners and the AFC’s Technical Study Group officers.
Endo played three AFC Asian Cup 2011 qualifiers this year as well as six AFC Champions League matches. He also played in three FIFA World Cup qualifiers for Japan.
He was able to earn 120 points from matches in 2009, thanks to six MVP titles. This was 20 more points than joint second-placed Sayed Mohamed Adnan and Nakamura.
Aghily finished with 95 points while Al Khatib ended up with 85.
Endo helped Japan qualify for the FIFA World Cup finals while Gamba, last year's Asian champions, reached the round of 16 this year before losing to fellow J.Leaguers Kawasaki Frontale 3-2.
"I would like to thank the AFC for this Award," said Endo, who was nominated last year but lost to Uzbek Server Djeparov. "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."
Photo: Yasuhito Endo receives his AFC Player of the Year Award from AFC President Mohamed Bin Hammam. - AFC.