The 40-year-old Namibian succeeds Ukrainian pole vault legend Sergey Bubka, whose term had come to an end.
"I've really enjoyed my time leading the Athletes' Commission," said Bubka.
"It's the best job in the IOC because you have the honour to represent the voice of the athlete. I think Frankie will take the Athletes' Commission to the next level. He's a perfect fit for the role."
Fredericks, whose only major title was the 1993 200m world championships crown though he also won three world silvers at the same event, took silver in the 100m and 200m at both the 1992 and 1996 Olympics. In the latter he had to give second best to world records set by Donovan Bailey and Michael Johnson respectively.
