Gili's highest profile appointment was as manager of Côte d'Ivoire. He was named as the Ivorians' head coach in January 2008, following the resignation of Ulrich Stielike due to personal reasons on the eve of the 2008 Africa Cup of Nations. Gili was promoted from within, having been a former coach of the country's Under-23 side with whom he qualified for the 2008 Olympics in Beijing.
After leaving the Côte d'Ivoire job, Gili was named manager of Qatari side Umm Salal, but he was sacked in 2010, leaving him unemployed for a year. However, he was reinstated on December 15, 2011 after Umm Salal sacked Moroccan coach Hassan Harmatallah 'for unhealthy working environment'. The team was at the bottom of the table with no wins so far in mid-season. After the 2011-12 season, Gili was replaced by another French coach Bertrand Marchand.