In the summer of 1986, Clarke made the big move of his career in a transfer to First Division club Southampton for £500,000, and he was an instant success in his first campaign as a top division striker with 20 league goals, including two hat-tricks in the first few weeks of the season. The Saints reached the semi-finals of the Football League Cup that season. He enjoyed another successful campaign a year later by scoring 16 goals, but a sudden loss of form in 1988–89 restricted him to nine First Division games (in which he failed to score).