The 21 year-old, who clinched the Scottish Premier League title last season, trailed two athletes; overall winner Rudisha and second placed Kemboi
The Scottish-based defensive midfielder was perceived a strong contender to clinch the top gong during the ninth edition of the ceremony, but settled for third position after a competitive voting and scrutinizing procedure handled by a panel of respected sportsmen and athletes, as well as an independent online voting system.
The 21 year-old, who won the Scottish Premier League title last season, trailed two athletes; overall winner David Rudisha, who is the reigning 800m record holder as well as the World and Olympic Champion over the distance.
3000m steeplechase Olympic and World Champions Ezekiel Kemboi emerged second.
"I am delighted and satisfied with this achievement. This is the first time I was nominated for any local award. I also congratulate Rudisha and Kemboi for the success. Bottom line and most important is that we are all proud after placing out country on the World map," Wanyama told Goal.com.
The SOYA annual award is given to Kenyan sportsmen and women who have brought success and recognition to the country.
Wanyama will be hoping for more glory during the Continental Caf awards set to take place in Ghana later this month.
The former Beerschort SC (Belgium) ace is competing against Egypt's Mohammed Salah and Senegal's Papa Moussa Konate in the Most Promising Talent category.