2011-12: Michael Prapavessis skated for the Mississauga Rebels minor midget AAA team in Greater Toronto. He scored 6 goals with 15 assists and had 18 penalty minutes in 53 games. Prapavessis played for the Rebels in the 2012 OHL Cup and in seven games he scored 1 goal with 3 assists. He was selected by Saginaw in the 10th round (194th overall) of the 2012 OHL Priority Draft and was taken by the Lincoln Stars in the sixth round (78th overall) of the 2012 USHL Futures Draft.
2012-13: Prapavessis split the year between the junior A Toronto Lakeshore Patriots and the Mississauga Rebels midget AAA team. In 25 regular season games with the Patriots he scored 2 goals with 9 assists and 2 penalty minutes. Prapavessis had 3 assists and 2 penalty minutes in six playoff games. He scored 3 goals with 6 assists and 4 penalty minutes in 26 games with Mississauga. In February he committed to playing college hockey at RPI in 2014-15.
2013-14: Prapavessis returned to the Toronto Lakeshore Patriots for his first full season in the Ontario Junior Hockey League and participated in the 2013 RBC Cup (Canada Junior A championship) as the Patriots captured the league playoff and Dudley Hewitt Cup playoff titles. After scoring 5 goals with 49 assists and 2 penalty minutes in 47 OHJL regular season games, Prapavessis scored 2 goals with 13 assists and 4 penalty minutes in 19 playoff games. In nine games in the Dudley Cup and RBC Cup playoffs he scored 4 goals with 4 assists and 4 penalty minutes. The Patriots finished fifth in the RBC Cup. Prapavessis skated for the Canada East squad in the 2013 World Junior A Challenge and had 2 assists in four games. Ranked 108th amongst North American skaters in the Central Scouting final rankings he was selected by Dallas in the fourth round (105th overall) of the 2014 NHL Draft.