Duncan, who has won the Currie Cup as captain of the 2007 Free State Cheetahs team, served as not only Director of Rugby but also as head coach of the Currie Cup and PRO14 side and has been an vital part of the Cheetahs over the last four years.
He has made a lasting impact not only on the filed but also in the boardroom.
During his tenure as Director of Rugby, Duncan played an integral part in opening the doors for the Cheetahs in the northern hemisphere and has gone on to coach the team to eight victories thus far in the 2017/2018 PRO14.
"We have great appreciation for what Rory has done for Free State Rugby over the last four years and we wish him well," said Harold Verster, Manging Director of the Free State Cheetahs.
Free State Rugby thanked Duncan for his commitment and dedication during his time at the Cheetahs and is "proud to send yet another product of the Cheetah into the rugby world and wish him well on his future endeavours".
Meanwhile, the Cheetahs have welcomed the return of Franco Smith to succeed Duncan.
The Cheetahs are currently third in Conference A in the PRO14, having won eight of their 13 games.
They will face the Cardiff Blues in Wales on Saturday, February 10 21:35 (SA time).