Ganaye will start work as president at Nice on Friday, co-owned by Barnsley owners Chien Lee and Paul Conway.
Restructuring at the club at operational level recently saw president Jean-Pierre Rivère and chief executive Julien Fournier leave their positions - with Frenchman Ganaye tipped to be part of the new-look set-up at the Allianz Riveira
Ganaye was keen to pilot Barnsley through the transfer window and will finish his duties at Oakwell after tomorrow’s window deadline.
Reds chairman Paul Conway will take on Ganaye’s responsibilities for an initial period ahead of a future announcement on his long-term successor as CEO.
On his departure, Ganaye - who became English football’s youngest chief executive when he joined the Reds at the age of just 30 in the summer of 2016 – said: “I will always be grateful to Patrick Cryne for giving me the opportunity to become chief executive of this great club. I have enjoyed every minute of my time here and I believe that we have built something together that everyone can be proud of.
“It was important for me to make sure this transfer window was completed before leaving, allowing Daniel (Stendel) and his staff to remain at the club with the best possible chance of promotion back to the Championship this season.
“From day one of me moving to Barnsley, everyone in the community welcomed me and my family and we leave after 20 months, feeling part of the community here. I have met many of you in and around the town or at games, my son has been raised here since he was born, and my wife has made friends for life amongst you.
“This is not us leaving, we are just moving and we will remain on the journey with you.”
In a statement, Conway said: “Gauthier has been an incredible servant to the club and the Barnsley community.
“He has worked tirelessly to strengthen our club both on and off the pitch. Gauthier will always be part of the Barnsley family and we look forward to seeing him at Oakwell.”
“To ensure a seamless transition and continue the club’s goal of automatic promotion this season, I will assume Gauthier’s responsibilities until we can make a further announcement.”