 In January 2008 Whelan joined Stoke City for a fee of £500,000 with whom he helped gain promotion to the Premier League.He took a while to establish himself in Tony Pulis' first team plans in the top flight but by 2009 he became a regular and went on to play in the 2011 FA Cup Final, but his old club Manchester City beat Stoke 1–0.Whelan continued to be a regular in the side under Pulis and kept his place under Mark Hughes.