Fernando made his debut with the main squad on 15 January 1984 in a 1–2 away loss against Real Valladolid, after moving up from the reserves CD Mestalla. He truly came to the forefront in 1986–87 as the team won promotion back from Segunda División at the first attempt; aside from this campaign he spent all of his spell with Valencia in the top flight, where he twice finished second in the championship, also helping to a runner-up finish in the Copa del Rey of 1995.