Yates was a cult hero at Tranmere, and is best remembered for scoring two goals in a Merseyside derby against Everton at Goodison Park when Tranmere beat the Premier League outfit 3–0 in the 2000-01 FA Cup. That same season he also scored one of the goals as Tranmere knocked Leeds United out of the League Cup. Yates remained with the club until 2002 when he transferred to Sheffield United. Whilst at Tranmere he played in the 2000 Football League Cup Final, coming on as a substitute in the final against Leicester City.