Mbappe left a PSG team last summer for Real Madrid which finished this past season as Quadruple winners of the Champions League, Ligue 1, Coupe de France and French Super Cup titles.
Asked if he regretted not having Mbappe with PSG last season, Al-Khelaifi said: "I don't regret it. I think I have to thank Kylian , honestly, because he's also given a lot to the club.
"Him, Messi, Neymar, Ibrahimovic, all the players... Because it was a very important period for the club.
"We're lucky this year without him, but I also wish him the best, because I have great respect for the big stars, the great players. Even if we have a small conflict, honestly, from the bottom of my heart, I wish him the best."
Al-Khelaifi then smiled on France 5's 'C à vous' programme: "What I don't wish him is the best when he plays against us!"