Anderton was signed as an apprentice by Portsmouth manager Alan Ball, coming to prominence at 18 when he scored at Anfield in an FA Youth Cup match against Liverpool which ended 2–2. His first team debut came against Cardiff City in the second round of the League Cup in October 1990 as a substitute for youth team colleague Darryl Powell. Anderton made his full league debut against Wolverhampton Wanderers in a 0–0 draw, making 20 appearances in the 1990–91 season. Under new manager Jim Smith, Anderton became a regular in the attacking side of the 1991–92 season, scoring his first club goal in the season opener against Blackburn Rovers. His performances soon drew the attention of bigger clubs and after an impressive FA Cup run, during which he scored in a semi-final clash with Liverpool, he joined Tottenham Hotspur for £1.75 million in 1992.