The Frenchman becomes the second AFCON 2017 coach to resign
The defending champions bowed out of the group stage in the ongoing Africa Cup of Nations in Gabon, failing to manage a single win against Togo, the DRC and Morocco.
The Ivorian FA saluted the 57-year-old for his "professionalism, commitment and human quality", adding that plans are in place to find his successor.
"The appropriate measures will be put in place to find his successor," a statement said.
The former Guinea and Benin coach was in charge of the Elephants for 18 months. He succeeded compatriot AFCON winner Herve Renard in July 2015.
He becomes the second AFCON 2017 coach to resign after Algeria's Belgian coach Georges Leekens.