Fernández moved to Valencia CF in 2006, being named manager of the Juvenil squad. In July of the following year, he was appointed at the helm of the reserves in the fourth division,[2] and on 29 October 2007, after Quique Sánchez Flores was sacked from the main squad, he was appointed interim.[3] His first professional match occurred two days later, a 5–1 loss against Real Madrid.[4]
Fernández managed the Che for one further match, a 2–0 away defeat of RCD Mallorca,[5] and subsequently returned to the B-team after the appointment of Ronald Koeman.[6] He left the club in 2010, and spent a year without work before being appointed at newly formed side Huracán Valencia CF in June 2011.[7]
On 16 June 2011, Fernández announced his departure from Huracán, after having accepted an offer from Superleague Greece side Asteras Tripoli FC.[8][9] In September, however, after only three matches, he was sacked.
On 24 October 2011, Fernández returned to Spain and was presented as manager of fourth division side CF Gandía.[10] On 20 September of the following year, he moved to Qatar to work for Aspire Academy, being manager of the national under-17 team.[11][12]
On 10 July 2015, Fernández was appointed manager of Atlético Madrid's Juvenil A squad.[13] Roughly one year later he took over the B-team,[14] achieving promotion to Segunda División B in 2017 and reaching the third division play-offs in 2019.
On 15 June 2019, Fernández was named UD Almería manager in Segunda División, replacing departing Fran Fernández.[15] On 3 August, however, after the club's change of owner, he reached an agreement to terminate his contract.[16]
On 4 August 2020, Fernández returned Valencia and its reserve team, with the side now in the third division.[17] He left the club the following 17 June, and returned to Almería four days later, now named manager of the B-team in Tercera División RFEF.[18]
