 Despite being offered a new contract with Grimsby, Atkinson opted to transfer to fellow Conference Premier side Fleetwood Town on 10 June 2011.In his first season with the club Fleetwood earned promotion to the Football League for the first time in their history.The following season Atkinson spent time on loan with Accrington Stanley but following a managerial change at Fleetwood he returned to the club and briefly captained the side.