2009-10: Michael Clarke skated in one game for the London Junior Knights midget AAA team and was the second-leading scorer for the Knights' Gold midget minor team. The Knights Gold finished first in the West Division of the Ontario Midget Minor Alliance and in 27 games Clarke scored 15 goals with 18 assists and had 12 penalty minutes. In the Alliance playoffs he scored 7 goals with 7 assists and had 25 penalty minutes in 12 games. Clarke was selected by the Windsor Spitfires in the second round (38th overall) of the 2010 OHL Priority Draft.
2010-11: Clarke appeared in nine games (including one playoff contest) with the OHL's Windsor Spitfires after skating in the Greater Ontario Junior A league with the London Nationals for most of the season. Clarke saw limited ice time in eight regular season games in November and December for the Spitfires and was minus-four with no points or penalties.He made his lone playoff appearance in Game 4 of Windsor's second round series with Saginaw. In 39 games with the Nationals he scored 14 goals with 22 assists and had 29 penalty minutes. London finished second in the Western Conference and reached the conference finals. In 12 playoff games Clarke scored 6 goals with 3 assists and had 8 penalty minutes.
2011-12: Clarke saw significant ice time for Windsor in his second season with the Spitfires and emerged as a physical, two-way forward with some offensive elements to his game. In 68 games he scored 15 goals with 21 assists and was third on the team with 81 penalty minutes while finishing minus-six. In what was a rebuilding year for the Spitfires (Windsor was second in the West Division and reached the playoff semifinals in 2010-11 and won back-to-back Memorial Cups in 2009 and 2010), Windsor finished fourth in the West and were swept by London in a first-round playoff series. In the four-game series with the Knights Clarke scored 1 goal and was plus-one with 4 penalty minutes. Clarke was ranked 119th amongst North American skaters in Central Scouting's final rankings (after being rated 66th in the mid-season rankings) and was selected by Colorado in the fifth round (132nd overall) of the 2012 NHL Draft.
2012-13: Clarke returned to Windsor to start his second full OHL season but was obtained by Peterborough in the trade deadline deal that sent defensmen Slater Koekkoek, a first round pick by Tampa Bay in 2012, to the Spitfires. Clarke scored 8 goals with 11 assists in 34 games with Windsor and was -11 with 28 penalty minutes. In 28 games with the Petes he scored 7 goals with 6 assists and was -12 with 18 penalty minutes. Peterborough finished fourth in the East Division, missing the OHL playoffs for the third straight season.