Son of Brazilian parents, Fernándes moved from his native Tocopilla to Calama at the age of six, where he attended school along with his brother Christian. There, they participated in sports and music. While he lived in Calama, he joined the lower divisions of Cobreloa, participating in each of their youth categories and was integrated to Cobreloa's B team that participated in the Chilean Third Division during the 2006 season. In this period of time, he shared team and home with countryman forward Alexis Sánchez. Later, in 2007, he was sent on loan to Mejillones after Cobreloa gave up their reserve team. After the request of coach Lewis Sheldon, Fernándes joined Cobreloa's first team to face the Clausura tournament. His professional debut came in the fourth round of the championship, when he replaced strikerFelipe Flores in a match that would end with a 2–1 victory over La Serena. His first time as a starter was in a game against Melipilla, which ended in a 5–1 victory, with Fernándes scoring a hat trick.
In 2010, he played for Magallanes of the Chilean Tercera División A where he became the figure of the team that won the championship and was promoted to the Primera B. His outstanding performance on Magallanes caught the attention of Palestino, joining them in 2011, and thanks to his good results, he later was nominated for the Under 25 Chile national football team.
On 2 December 2011, Palestino agreed on the sale of 50% of his pass with a US$700,000 transfer to Universidad de Chile aiming to win the 2012 Apertura tournament, and thinking that the team will play Copa Libertadores next year. On 5 December, he was presented in the offices of "the Blues" Sports Complex with the No. 9 jersey. Fernándes made his debut for the club, scoring and providing an assist in a 3–1 win over Deportes La Serena on 4 February 2012. In the league, he would score five goals. In the play-offs Apertura, Fernándes scored a hat-trick in a 4–0 win over Colo-Colo on 24 June 2012. Elsewhere in the Copa Libertadores, Fernándes scored a hat-trick and set up a goal in a 5–1 win over Godoy Cruz and soon scored a brace and providing an assist in a 6–0 win over Deportivo Quito. Soon after scoring goals, he would received criticism over his performance.
Bayer Leverkusen
On 6 July 2012, he signed for Bundesliga squad Bayer 04 Leverkusen from Universidad de Chile for a transfer fee of €7 million and a five-year contract. Fernándes made his debut for the club, scoring on his debut in first round of DFB-Pokal in a 4–0 win over Carl Zeiss Jena; seven days later, he made his debut, coming on as a substitute, in a 2–1 loss against Frankfurt. However, in his first season, Júnior Fernándes playing time was reduced, as well his first team and haven't scored his first goal for the club.
On 26 May 2013, it was announced that Fernándes signed a one-year-loan contract with the Croatian club Dinamo Zagreb. On 23 April 2014, following the end of his loan spell, Fernándes signed a six-year contract with Dinamo Zagreb.
Alanyaspor
In January 2017 he was loaned to Alanyaspor until the end of the 2016/17 season. He returned to Dinamo and scored 2 goals against defending league champion Rijeka. However, as Dinamo failed to qualify into Europa League, they sold him to Alanyaspor, now as a permanent transfer instead of a loan.
