2011-12: Alexis Vanier skated for the College Charles-Lemoyne Riverains in Quebec in his first season of midget AAA hockey. He scored 4 goals with 10 assists and had 110 penalty minutes in 34 games. The Riverains finished fourth in the Reebok Division. Vanier was selected by Baie-Comeau in the first round (13th overall) of the 2012 QMJHL Entry Draft.
2012-13: Vanier made his QMJHL debut as a 16-year-old with Baie-Comeau. He had 8 assists and was +9 with 66 penalty minutes in 53 regular season games on a veteran Drakkar defense corps. Baie-Comeau finished first in the East Division and reached the QMJHL Finals against Memorial Cup champion Halifax. Vanier played in six of 18 playoff games; finishing with an even plus/minus, no points, and 2 penalty minutes.
2013-14: Vanier displayed an offensive component to his game; scoring at a point-per-game pace for Baie-Comeau in his second QMJHL season. Vanier skated for the QMJHL in the 2013 Subway Series against Russia and was selected to play for Team Cherry in the 2014 CHL/NHL Top Prospects Game.