Murphy started his professional career at Premier League side Middlesbrough in 2001, and remained at the club for three years, making sixteen appearances. During his time at Middlesbrough, he also had a loan spell with Division Two side Barnsley in 2004, where he made ten appearances. He left Middlesbrough for Scottish Premier League side Hibernian in the summer of 2004, and made 134 appearances for the club, before signing for Birmingham City in January 2008. He played 132 matches for the club in all competitions, and was an unused substitute as they won the 2011 League Cup Final, but his six-year stay was blighted by injuries, and he retired from football on medical advice in March 2014.