He missed two months at the start of the 2008–09 season with a thigh injury sustained in a 3–1 defeat at Swansea City on 16 August. He scored his first goal in the Championship with a "fine free-kick" in a 2–1 defeat at Queens Park Rangers on 18 October. On 2 November, he was sent off for a rash tackle in a 1–1 draw at East Midlands rivals Derby County. He was voted the 16th best player outside the Premier League in January 2009. However two months later new manager Billy Davies dropped him from the starting eleven after feeling McGugan was unfit and overweight.