In the 2016–17 season Fleury played 38 games and accumulated 18 wins. When Matt Murray was injured during warm-ups of Game 1 of the playoffs versus the Columbus Blue Jackets, Fleury took the starting position and led the Penguins to a 3–1 win. Fleury continued to lead the Penguins through the series, and his 49 saves on 51 shots in Game 5 helped the Penguins win the series against the Blue Jackets 4–1. With Murray out, Fleury continued to be the starter for the Penguins through the second round versus the Washington Capitals. The Penguins defeated the Capitals in seven games, with Fleury shutting them out in Game 7, and advanced to face the Ottawa Senators in the Eastern Conference Finals. Following a 5–1 loss in Game 3, the Penguins opted to go with a healthy Murray, who remained the team's starter en route to a Stanley Cup championship victory, defeating the Nashville Predators in six games. The win was the third Stanley Cup of Fleury's career.