The son of Brazilian parents, Fernandes, moved from his native Tocopilla to Calama at the age of six, where he attended school along with his brother Christian.

His professional debut came in the fourth round of the championship, when he replaced striker Felipe Flores in a match that would end with a 2–1 victory over La Serena.

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.

[3] 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.

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.

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.

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.