Fernández made his professional debut for Defensa y Justicia on 25 May 2012 in a 1–0 loss to Ferro Carril Oeste. He participated in three matches but did not score a goal. In the following season Fernández participated in 13 matches, still without scoring.

In the 2013–14 season he secured a position as a starter and scored 11 goals including the goal that secured promotion for his club to the Primera División, against San Martín de San Juan on 15 May 2014. On 8 August 2014 he scored his first goal in the Argentine top division in a 3–1 loss to Racing Club.

On 31 December 2014 Fernández was signed by Racing Club for a reported $1 million in exchange for 50% of his economic rights. His first goal for the club was in the Copa Libertadores group stage against Sporting Cristal on 10 March 2015. He scored three goals in the competition before his club was eliminated by Guaraní in the quarter-finals. Fernández scored both goals in a 2–0 victory for Racing in his debut in the 2014–15 Copa Argentina against Independiente de Neuquén.

Fernández tested positive for cocaine at two in-competition controls in May 2015, and was subsequently handed a three-month ban from sports by AFA, with the ban ending 3 September 2015. The South American Football Confederation (CONMEBOL) did however seek a two-year ban for him, and he was still suspended in late September 2015. On 28 October it was announced that he had been banned for two years. The substance he had tested positive for was cocaine.

Due to all of those positive drug results, he was moved to Racing Club’s reserve team in 2016.

After a slow return to Racing’s professional squad in 2017, manager Diego Cocca had Fernández loaned out to Primera División side Sarmiento in May. For the club, he scored three goals in his first three matches. He played five of six remaining league matches for Sarmiento, who were relegated at the end of the season.

Fernández was recalled to Racing Club after his loan. He scored against Independiente Medellín in the second round of the 2017 Copa Sudamericana on 27 June 2017.

On 23 August 2017, Fernández joined Ligue 1 side FC Metz on a one-year loan deal. Metz secured an option to sign him permanently. He made seven substitute appearances for the senior squad without scoring before being moved the reserve squad in the Championnat National 3 (fifth division) for the remainder of the 2017 calendar year. In January 2018 his loan deal was terminated.

On 4 January 2018, Fernández was loaned from Racing Club to newly-promoted Chilean Primera División club Unión La Calera with an option to buy. The 23 year-old scored 11 goals in 12 league matches for Unión La Calera, helping to deliver one of the best seasons in the club’s history. His final match for the club was on 29 May against Colo-Colo, in which he scored in the 2–0 victory. Unión La Calera were 3rd place in the league at the time of Fernández’s departure to Mexico.

On 7 June 2018, Liga MX club Necaxa confirmed the signing of Fernández on a three-year contract from Racing for a reported $3 million. Fernández scored in his Necaxa debut in a 2–1 victory against Club América in the first round of the 2018–19 Apertura season. He scored four goals in 15 Torneo Apertura appearances, and twelve goals in 15 Torneo Clausura appearances, as well as two goals in two Copa MX appearances, both scored as a substitute in a 3–2 loss to Atlético San Luis. Necaxa qualified for the Clausura Liguilla playoffs, but Fernández did not participate because a transfer agreement for him had been reached.

On 6 May 2019, it was announced that Fernández had signed for Major League Soccer side Portland Timbers as a Designated Player for an undisclosed fee reported to be between $10 and $12 million, a Portland Timbers record. Fernández netted one goal in his debut against the Houston Dynamo on 16 May, and scored eight goals in his first six matches for the Timbers.

On 7 October 2019, it was announced that Fernández has voluntarily entered MLS’ Substance Abuse and Behavioral Health Program. On 15 November 2019, Major League Soccer announced they had terminated his contract.

Following his dismissal by Portland, Fernández moved back to his native Argentina, joining Argentine Primera División side Colón on 10 January 2020.