Born in Oldham, Lancashire, Pemberton started his career as a junior at Manchester United but was released in June 1983. He signed for Chadderton, then Rochdale before moving to Crewe Alexandra in 1985. He initially came to prominence when he joined Crystal Palace in 1988, helping them win promotion to the First Division in 1989. He appeared for Palace in the 1990 FA Cup Final against Manchester United. The initial tie was drawn 3–3 after extra time, with United winning the replay 1–0 after extra time.