At the start of the 2016–17 season, Fernandes appeared in the first eight league matches of the season, including captaining two matches. This last until he was sidelined two occasions for Stade Rennais, due to suspension and then suffered an injury. Following this, Fernandes continued to remain involved in the first team for the club despite finding himself placed on the substitute bench towards the end of the 2016–17 season. Despite this, Fernandes was able to make his 100th appearances for Stade Rennais, coming against SM Caen on 14 May 2017, in a 1–0 win. At the end of the 2016–17 season, he went on to make twenty–eight appearances in all competitions.