Lynch was recently appointed as the chief financial officer of Rio Tinto, which means he will now be based in London.
He offered his resignation from the commission, however it was rejected by chairman Mike Fitzpatrick.
"He is a very valuable member of the AFL commission," Fitzpatrick said.
"Given his strong financial background, I felt it was important to retain Chris on the AFL Commission during what is an exciting time for the game."
"I also believe there is a distinct advantage in having an AFL Commissioner based in a major city such as London, and to be exposed to the trends, issues and challenges facing major sports in that part of the world," Fitzpatrick added.
Lynch, who played five games for Geelong between 1972 and 1974, joined the commission in 2008 and chairs its audit committee. He also served on its broadcasting sub-committee.
Fitzpatrick said that he and Lynch would review the role in 12 months.
