Kipyego completed the Amsterdam Marathon course in a time of 2:06:19 just four seconds faster than he ran last year.
The 29-year-old Kipyego beat his countrymen Ezekiel Chebii (2:07:18) and Mike Kigen (2:07:45) who finished second and third overall in the Amsterdam Olympic Stadium.
Joyce Chepkirui won the women's marathon race. The 27-year-old Commonwealth Games 10000m champion Chepkirui crossed the line in a time of 2 hours, 24 minutes and 11 seconds.
Chepkirui improved her previous personal best by nearly 5 minutes. Flomena Cheyech finished 25 seconds behind compatriot Chepkirui to take second place.
Australian Milly Clark finished third, almost five minutes behind the winner.