Later, in 2007, he was sent on loan to Mejillones (another third division team) after Cobreloa gave up their reserve team.

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. Fernandes 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, Fernandes 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.

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. Fernandes 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, Junior Fernandes playing time was reduced, as well his first team and haven’t scored his first goal for the club.

Fernandes was called up to the Chile national football team to face friendly matches during the second half of 2011 by team manager Claudio Borghi. He debuted officially in the national team on 11 September 2012, on a qualifying match for the 2014 FIFA World Cup against Colombia.

On 26 May 2013, it was announced that Fernandes signed a one-year-loan contract with the Croatian club Dinamo Zagreb. On 23 April 2014, following the end of his loan spell, Fernandes signed a six-year contract with Dinamo Zagreb.

In January 2017 he was loaned to Alanyaspor until the end of the 2016–17 season. He returned to Dinamo for the 2017–18 season and scored twice against defending league champion Rijeka. However, as Dinamo failed to qualify into Europa League, losing to Skënderbeu Korçë in the play-off round, he moved back to Alanyaspor on a permanent transfer.

On 19 August 2020, Fernandes joined Ittihad Kalba of the UAE Pro League.