Fernando was born in Málaga, Andalusia. After starting at hometown's Málaga CF, he finished his football grooming in the ranks of La Liga giants Real Madrid, going on to appear once for its first team in the 1999–2000 season, against Real Zaragoza. After that, Fernando joined Real Valladolidon loan as many Real Madrid canteranos would move to that club in that timeframe.
Betis
In the summer of 2002, Fernando signed with top division club Real Betis, scoring 15 goals in his debut campaign, with the team finishing in eighth place thanks greatly to his braces against Málaga, RCD Espanyol and Real Sociedad. He won the only trophy of his career in 2005, the 2–1 Copa del Rey success over CA Osasuna. On 27 June 2008, as his role with Betis was a lesser one from 2005 to 2008 – only ten matches in his last season – Fernando signed a four-year contract with Málaga, returning to his first youth club after 11 years.
Málaga / Later years
Fernando netted his first league goal for Málaga on 23 September 2009 against Espanyol, more than one year after arriving; however, this happened in a 1–2 away loss. Sparingly used in his debut season, he became a starter in 2009–10, scoring on five occasions. Fernando continued in the starting lineups in the 2010–11 campaign, under new manager Jesualdo Ferreira. In the second matchday, he scored twice in a 5–3 win at Zaragoza, the first goal coming after just 73 seconds; rarely used by the following coach, Manuel Pellegrini, he still contributed with 21 games as the Boquerones finally avoided relegation. On 21 August 2011, 32-year-old Fernando was released from his Málaga contract. He moved abroad for the first time on 4 February of the following year, joining several compatriots at Hungarian side Diósgyőri VTK; he retired from football in June 2013.
Fernando started working as a full-time manager in 2016, with amateurs CD El Palo which he had already coached briefly the previous year after starting out with their youths. Early into the season in Tercera División, he resigned. On 23 April 2018, Fernando was appointed at former club Diósgyőr with the purpose of avoiding relegation from the Nemzeti Bajnokság I, which was finally achieved. On 3 September 2019, with his team placed last in the standings and following a 1–0 defeat against Ferencvárosi TC at the Groupama Arena, he was dismissed.
