2010-11: Nathan MacKinnon played for Shattuck St. Mary's U-16 squad. In 34 games, he scored 39 goals and added 46 assists for 85 points, while also picking up 70 penalty minutes. MacKinnon played for Canada Atlantic at the 2011 World Hockey Challenge U-17 Tournament where he scored 5 goals and added 3 assists for 8 points in 5 games.
2011-12: MacKinnon played his QMJHL rookie season with the Halifax Mooseheads. In 58 games, he scored 31 goals and added 47 assists for 78 points while also tacking on 45 penalty minutes. In 17 playoff games for the Mooseheads, MacKinnon scored 13 goals and added 15 assists for 28 points. MacKinnon once again represented Canada Atlantic at the 2012 World Hockey Challenge U-17 Tournament, scoring 1 goal and adding 3 assists for 4 points in 5 games.
2012-13: MacKinnon skated in 44 regular season games for the Mooseheads in his second season, missing time with a knee injury and also when he was with Team Canada at the 2013 U20 World Junior Championship. He scored 32 goals with 43 assists and was plus-40 with 45 penalty minutes; captaining a Halifax team that had the QMJHL's best record and won 58 of 68 games in regulation. In the Mooseheads first eight playoff games he scored 3 goals with 12 assists and was plus-eight. In six games for fourth-place Canada at the WJC he had 1 assist and was minus-one with 4 penalty minutes. MacKinnon was ranked second amongst North American prospects in Central Scouting's mid-season rankings prior to the 2013 NHL Draft, and remained the second-ranked North American in the CSS final rankings.