Fernández was assigned to the Rostelecom Cup and the Trophée de France for the 2016–17 Grand Prix series. He trailed Japan's Shoma Uno after the short program at the Russian Grand Prix event, having tripled one of his quad attempts. In the free skate, Fernández produced three quads, two triple Axels, and received the first 200+ long program score of the season: 201.43. One week later, he won both the short program and the free skate at the French Grand Prix, despite a fall in each segment of the event – on a quad toe loop in the short program, and a triple Axel in the free skate. He collected 15 points from both events and qualified for the 2016–17 Grand Prix Final with maximum points.