Born in Manchester, Higginbotham started his career at his local club Manchester United. He made seven appearances at Old Trafford, winning the Intercontinental Cup, as well as having a loan spell with Belgian side Royal Antwerp before joining Derby County in order to play more matches. He spent three years at Derby but handed in a transfer request when the club was relegated from the Premier League. Southampton signed Higginbotham for a £1.5 million fee in February 2003, and he helped them reach the 2003 FA Cup Final. When Southampton were relegated in 2005, Higginbotham rejected a new contract and was placed on the transfer list.