The 51-year-old, who has been at the French club since 2009, will see his contract run out in the summer.
"After four great years, my adventure with Rennes is coming to an end," he told the club's official website.
"I've decided to leave the club, in part due to the disappointment caused by this difficult end to the season. I will nonetheless remember the many games in which we came so close to the success that has too often cruelly escaped us.
"Now, our duty is to not give up, and give everything on the pitch to end the season with our heads held high."
Rennes are currently 10th in Ligue 1 with 42 points from 32 matches.