Jones has previously played for Leyton Orient, Preston North End and Stevenage, and has had loan spells with Coventry City, Rochdale and Colchester United. On 7 August 2017, he signed for Wigan Athletic on a one-year contract after rejecting a new contract at Stevenage. Wigan entered into contract talks with him at the end of the 2017–18 season. He also became the club's captain, starting with 2020–21 season.
Jones was the goalkeeper for Wigan's League Cup campaign, which began with consecutive penalty shootout wins over Hull and Bolton. Jones took a penalty in both shootouts, and saved one in the second.