Fernández was born in Zaragoza, Aragon. Late into the 1990–91 season, aged only 30, he was promoted to hometown Real Zaragoza's first team, eventually leading it to the 17th league position and avoiding La Liga relegation in the playoffs against Real Murcia; at the time of his beginnings, he was the second youngest manager to ever coach in the category, after Xabier Azkargorta. In the following years, Fernández helped Zaragoza consolidate in the top division, notably reconverting Gustavo Poyet from forward to attacking midfielder and winning the Copa del Rey in 1994 and the UEFA Cup Winners' Cup in the next season. He was relieved of his duties on 8 November 1996, meeting the same fate the following year with his next club, CD Tenerife. For four complete seasons in the late 90s/early 2000s, Fernández was in charge of RC Celta de Vigo, helping the Galicians qualify three times for the UEFA Cup during his spell while playing highly attractive football. From 2002 to 2004 he worked with fellow top flight team Real Betis, respectively finishing eighth and ninth in his two years. In August 2004, Fernández moved abroad and joined Portuguese club FC Porto. He started his tenure with the conquest of the Intercontinental Cup, but was abruptly fired in January of the following year following a 1–3 home loss against S.C. Braga. Fernández returned to his beloved Zaragoza for the 2006–07 campaign, qualifying the side for the UEFA Cup in his first year but being sacked midway through his second, as the season eventually ended in relegation. In another return he joined Betis in late January 2010, replacing fired Antonio Tapia; during his spell the Verdiblancos were the team in the league with the most points, but they could not eventually promote from Segunda División, after finishing with the same points as the third-placed club. On 9 January 2013, Fernández moved for his second experience abroad, signing a contract with Belgium's K.A.A. Gent. He was sacked on 30 September 2013, due to poor results. Fernández was appointed as the new manager of Deportivo de La Coruña on 10 July 2014, succeeding Fernando Vázquez. He was relieved of his duties on 9 April of the following year, with the team eventually narrowly escaping relegation. In the summer of 2015, Fernández signed for Real Madrid as youth system coordinator. He left the Santiago Bernabéu Stadium in 2017, and on 17 December 2018 he returned to Zaragoza for a third stint as manager replacing the sacked Lucas Alcaraz.
