He made his 100th appearance for Stoke in a 2–0 win over Everton on 1 January 2011. After drifting in and out the starting eleven for most of the 2010–11 season Whelan made a return in March and has played a key role in Stoke's run to their first FA Cup Final. Whelan reached a century of league appearances for the club on 8 May 2011 against Arsenal. Whelan played in the 2011 FA Cup Final as Stoke lost 1–0 to his old club Manchester City.