Despite this investment, however, Fernández struggled to establish himself at Celtic, possibly because his thoughtful style of play did not fit in with the often direct approach of O'Neill's team. He scored his first and only goal for the team against FK Sūduva Marijampolė in the UEFA Cup, on 3 October 2002. After a first season spent almost exclusively on the bench, his future looked to lie away from Celtic, and he was loaned back to Livingston for 2003–04, where he was part of the side that won the League Cup after beating Hibernian 2–0.