Hughes made a total of 293 appearances for the Blues, scoring 42 goals, and was an essential part of Steve Bruce's side's playoff-winning season in 2002, and their first and second seasons in the Premier League, before his switch to south-east London. While at Birmingham he played in the 2001 Football League Cup Final as a substitute; although he scored his penalty, Birmingham lost the shootout 5–4. Having rejected a new deal with Birmingham, in July 2004 he moved to Charlton Athletic, signing a three-year contract.