 Whelan was again a key figure under Hughes in 2015–16, making 42 appearances as Stoke again finished in 9th position.He also filled in as stand-in captain during the season due to injury to Ryan Shawcross.He made his 300th appearance for Stoke on 12 March 2016 against Southampton, however he was not to be on the winning team as Stoke lost 2–1 at home.