Most famous for captaining Sheffield Wednesday, Atherton started his career at hometown club Wigan Athletic as a trainee and spent three years there before attracting the attention of Coventry City. Atherton was lured away from Wednesday by Bradford City after relegation on the Bosman ruling where he also spent a spell on loan at Birmingham City. Birmingham reached the League Cup final, however, Atherton was unable to play as he was cup-tied. After being released by Bradford on a free transfer he finished his career at Halifax Town, where injury forced him to retire from professional football after playing only 14 games for the club, but came out of retirement because of Halifax's injury crisis and was named as a substitute for their home game against Grays Athletic on 16 October 2007.