Rooney signed for Stoke City in the summer of 2005. In his first season at Stoke, Rooney made his debut at academy and reserves levels, before making his first team debut as a second-half substitute against Tamworth in the FA Cup. Rooney scored his first goal for Stoke against Reading on 17 April 2006. In only his second full start for Stoke City, he scored a hat-trick against already relegated Brighton & Hove Albion in the final fixture of the 2005–06 season to become Stoke's youngest ever hat-trick scorer (Stanley Matthews was the previous holder).
On 16 March 2007, it was announced that Rooney had joined Yeovil Town on loan for a month.