In 1990, Pemberton transferred to Sheffield United. During his début against Liverpool in the season opener, he was forced to play in goal after an injury to the United keeper. His most memorable moment came in 1993 when he scored the winning penalty in the shootout against Blackburn Rovers in the quarter-final replay in the FA Cup. The following summer, he was sold to Yorkshire rivals Leeds United. Pemberton became something of a cult figure at Leeds owing to his determination and high work-rate. He appeared in a second Wembley final when he played for Leeds in the 1996 League Cup Final against Aston Villa; again, unfortunately for Pemberton, his side was defeated.