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Hughes started his career with Scottish Premier League club Rangers at the age of 16. He went on to make 90 appearances for the Ibrox club and scored seven goals in the process. Hughes then joined Leicester City in January 2005 for £100,000. In summer 2007, Hughes was placed on the transfer list by then Leicester manager Martin Allen, with Hearts and Motherwell reportedly offering £50,000 for the player.After delays in a transfer to Hearts, Hughes joined Motherwell for an undisclosed fee.

Hughes joined Norwich City as a free agent in August 2009. Hughes left Norwich on a loan spell at MK Dons to gain fitness after an operation. He left Norwich by mutual consent in August 2011. After leaving Norwich, Hughes became a free agent, but failed to find a club in the first few months before re-joining Motherwell for six months. Then, after a short trial, Hughes signed for Aberdeen on 27 January 2012.Hughes has one cap for Scotland after he was called up to the Scotland squad to play Japan in October 2009.