Roy, who led one of the most unlikely success stories in recent European football, had kept his illness private for three and a half years.
Appointed in January 2023 after a decade away from management, Roy took charge of a Brest side widely expected to be relegated.
He guided the club to an unexpected third-place finish in Ligue 1 in the 2023/24 season, securing their first qualification for European competition and earning the league’s Manager of the Season award.
“His time at Stade Brestois was one of the most beautiful periods of his life. It gave him energy, joy and a reason to keep going, even through the most difficult moments,” his family said in a statement.
“With his players, he built a rare and wonderful bond. He loved them deeply, and he was proud, profoundly proud, to be their coach.”
Before moving into management and sporting director roles at clubs including Nice, Lens and Watford, Roy had a long playing career in the 1990s.
A defensive midfielder, he made more than 300 appearances in France for teams such as Nice, Lyon and Marseille, and also had a spell with Sunderland in the Premier League.