Khalikhodzic is an experienced football coach, and he has made many achievements in his coaching career. He has been the head coach of clubs and national teams in many countries, including Beauvais in France, Casablanca Raja in Morocco, Lille, Rennes, Paris Saint-Germain, Trabzon Sports Team and Etihad.

During his coaching career, he led many teams to win honors. For example, during his coaching in Morocco, he led Casablanca Raja to win the Moroccan League championship of 1998 and the African Champions Cup of 1997.