"(I'm) somewhat surprised, but very honored," McIlroy said, according to the Associated Press' Doug Ferguson.
The 30-year-old Northern Irishman won the Players Championship and Canadian Open, and also won the Tour Championship to secure his second FedEx Cup trophy. McIlroy finished the season with an astounding 14 top-10 finishes in 19 events played.
He was previously named Player of the Year in 2012 and 2014.
McIlroy's win marks the first time since 1991 that different players received the PGA Tour's and PGA of America's respective Player of the Year awards. Koepka captured the PGA of America's honor, which is based on a point system, for his brilliant performances in major championships.