Beginning his career with Paris Saint-Germain, Fernandez was loaned to LB Châteauroux to experience first-team football. When he returned to PSG, he became sub for Bernard Lama, and then Dominique Casagrande. The 1997–98 season was one of his best, because even though he did not play much in the championship, he still won two cups. In 1998 FC Sochaux, who had recently reached Ligue 1, offered him a place, which he took up and kept until Teddy Richert convinced him to play for RC Strasbourg. He played there for two years, but did not manage to shine, so he moved to the Ligue 2 side Châteauroux. He played for the club as starting goalkeeper for 8 years.