Clarke was transferred to Chelsea for £422,000 in February 1987. He stayed at Chelsea until 1998, making 421 appearances. He was a part of the Chelsea sides which won the 1997 FA Cup Final, 1998 Football League Cup Final and 1998 UEFA Cup Winners' Cup Final. The latter match, against VfB Stuttgart in Stockholm, was Clarke's final appearance for the club. In 2005, he was voted into Chelsea's centenary XI, occupying the right-back berth.