At the start of the 2015–16 season, Fernandes started in the next first four league matches of the season. This last until he was suspended for picking up five yellow cards, having picked up three bookings in the last three matches. After serving a one match suspension, Fernandes returned to the starting line–up against Lille on 19 September 2015, as Stade Rennais drew 2–2. However, his return was short–lived in a follow–up match against Gazélec Ajaccio when he suffered a muscle injury and was substituted in the 22nd minutes, as the club drew 1–1. After the match, it was announced that Fernandes was sidelined between three to four weeks. It wasn't until on 18 October 2015 when he returned to the starting line–up against Nice, as Stade Rennais lost 4–1. Fernandes then captained the club for the first time in his career against FC Lorient on 24 October 2015 and helped the side drew 1–1. Two weeks later on 6 November 2015, he scored his first goal for Stade Rennais, in a 2–0 win against Angers SCO. Fernandes then made his 50th appearances for the club, starting the whole game, in a 1–0 loss against Marseille on 3 December 2015. Since returning from injury, Fernandes continued to establish himself in the starting eleven, playing in the midfield position. Despite missing two more matches later in the 2015–16 season, due to suspension, Fernandes went on to make thirty–seven appearances and scoring once in all competitions.