He joined fellow Championship side Stoke City for a £225,000 fee in August 2006. He was made captain when Michael Duberry left in January 2007 and Stoke went on to narrowly miss out on a play-off place. With Stoke not being promoted Higginbotham again decided to hand in a transfer request to help force through a move to Sunderland. He spent one season at the Stadium of Light before returning to Stoke in 2008. He became a vital member of Tony Pulis' squad as Stoke established themselves in the Premier League. He scored the winning goal in the FA Cup quarter-final against West Ham United but missed out on both the semi-final and the final due to a knee injury. After his recovery he struggled to force his way back into the side and spent time out on loan to Nottingham Forest and Ipswich Town before joining Sheffield United on a free transfer in January 2013. After eight months at Bramall Lane, he left to join Conference Premier side Chester before ending his career with a short spell at Altrincham.