Federico has Italian origins: his maternal great-grandfather was a native of Lacedonia, in the Province of Avellino. As a result, he has an Italian passport.
Club career
Estudiantes
Fernández made his league debut for Estudiantes de La Plata on 14 September 2008 during the 2008 Apertura tournament in a 1–0 defeat to Vélez Sársfield. He played two games in Estudiantes' run to the final of Copa Sudamericana 2008. Fernández scored his first goal with the squad in an away match against Lanús on 2 May 2009, following an assist by teammate Juan Sebastián Verón. Later that year, Estudiantes won the 2009 Copa Libertadores, although Fernández's only contributions were two substitute appearances against Defensor Sporting Club in the quarter-finals.
Napoli
Fernández was signed by Serie A club Napoli in December 2010 for a reported fee of about €2.5 million. Due to his lack of a European Union passport, however, he arrived in Italy only in July 2011. On 2 November 2011, Fernández scored his first two goals for Napoli, against Bayern Munich in a Champions League group stage away tie. Both headers came after Napoli had conceded three times in the first half, although Napoli lost the match 3–2. Having only made nine appearances across all competitions for Napoli that season, on 31 January 2013 Fernández was loaned to Spanish La Liga club Getafe for the remainder of the campaign, bolstering the club's defence following the sale of David Abraham to 1899 Hoffenheim. Fernández played the full 90 minutes of the 2014 Coppa Italia Final, which Napoli won 3–1 against Fiorentina.
Swansea City
On 20 August 2014, it was announced that Fernández had signed for Premier League side Swansea City on a four-year contract for €10 million. Six days later, he made his debut for the club, playing the entirety of a 1–0 win over Rotherham United in the second round of the League Cup. His first Premier League appearance for Swansea was on 13 September, replacing Jordi Amat at half-time in a 4–2 defeat away to Chelsea. Fernández was given a straight red card for a foul on Philippe Coutinho in added time at the end of Swansea's League Cup fourth-round match against Liverpool at Anfield on 28 October; minutes later, Dejan Lovren scored the winner to knock Swansea out of the tournament. Two days later, however, the FA rescinded the red card on appeal from Swansea, thus avoiding a three-match ban for Fernández. On the opening day of the 2015–16 season, he scored an own goal vs Chelsea, in a match that ended 2–2 at Stamford Bridge. He scored his first goal for Swansea on 19 March 2016 in a 1–0 victory over Aston Villa at the Liberty Stadium.
Newcastle United
On 9 August 2018, Fernández joined Newcastle United on a two-year contract. The move reunited him with Rafa Benítez, his manager when both were at Napoli. He scored his first Premier League goal on the 2nd of November 2019 in a 3-2 away win at West Ham. His second NUFC goal came in a 2-1 Premier League home win against Southampton.