2009-10: Sebastien Auger played for the Quebec midget AAA regular season champion Seminaire St-Francois Blizzard; sharing the goaltending duties with Maxime Legace. In 22 regular season games he was 14-5 with two shutouts and had a 2.74 goals against and .907 save percentage. Auger appeared in one playoff game and was 0-1, allowing 4 goals on 30 shots. College Esther-Blondin defeated the Blizzard in four games in a preliminary round best-of-five series. Auger was selected by St. John in the fifth round (74th overall) of the 2010 QMJHL Entry Draft.
2010-11: Auger returned to Seminaire St-Francois for his second season with the Blizzard. He appeared in 28 of 41 games as the Blizzard slipped to last in its division. Auger was 7-14 with a 3.53 goals against and .886 save percentage. Auger started three of four playoff games and was 1-2, with one of the losses coming in overtime, and had a 2.07 goals against and .918 save percentage.
2011-12: Auger appeared in 22 games for the defending Memorial Cup champion Saint John Sea Dogs as a backup to 20-year-old Mathieu Corbeil-Theriault in his first QMJHL season. He was 14-4 with two shutouts and had a 2.65 goals against and .897 save percentage. The Sea Dogs finished first in the Maritimes Division and won the QMJHL playoff championship to reach the 2012 Memorial Cup. The Sea Dogs fell to QMJHL rival Shawinigan, the host team, in the semifinals. Auger did not play in the post-season.
2012-13: Auger took over as the starter for Saint John in his second season as the Sea Dogs slipped to fifth in the Maritimes Division. In 56 regular season games he was 22-32 and had a 3.33 goals against and .907 save percentage. Auger had a 6.00 goals against and .883 save percentage in four playoff games as Saint John was swept by eventual Memorial Cup champion Halifax.
2013-14: Auger returned to Saint John for his third season with the Sea Dogs. Appearing in 55 of 68 games he was 15-33-5 with two shutouts and had a 3.18 goals against and .915 save percentage. One of the youngest teams in the QMHL, Saint John finished last in the Maritimes Division and missed the playoffs with the league's second-worst record.