Joining Everton in the closing months of the 1986–87 season, Clarke quickly established himself as a key member of Everton's championship-winning side scoring five goals in ten games, notably the winning goal away at Arsenal not long after he joined, and earning himself a championship medal. He then began the following season with the only goal in a 1–0 Charity Shield win over FA Cup winners Coventry City at Wembley, and later scored the only goal in the Merseyside derby that not only beat arch-rivals Liverpool, but also prevented them setting a new record of 30 games unbeaten from the start of a season. However, with Graeme Sharp and Adrian Heath being Everton's main striking partnership, Clarke's appearances for Everton in the 1987–88 and 1988–89 seasons were largely limited to coming on from the substitute's bench or covering for Sharp or Heath when they were injured. He helped Everton reach the FA Cup final but did not play in the final (which Everton lost to Liverpool), following which Everton brought in Mike Newell from Leicester City in part exchange for Clarke and £500,000.