Koepka also won the award last year.
The two-time PGA champion defended his title earlier this year at Bethpage Black and won two other tournaments. McIlroy, who won the Tour Championship on Sunday, also won three times. McIlroy won the Vardon Trophy for lowest adjusted scoring average.
Koepka earned 50 of his 84 points for capturing the PGA and also won the CJ Cup and the WGC-St. Jude Invitational as well as top-four finishes in the other majors. He also topped the season money list and was fourth in the Vardon Trophy for adjusted scoring average.
The PGA Tour also awards a player of year honor that is voted on by the players.