2010-11: Alexis Pepin appeared in his first midget AAA game as a 15-year-old — playing most of the seasons with the Predateurs du St. Laurent bantam team — and attended the initial NHLPA All-Canadians Mentorship Camp in August. He had no points with 8 penalty minutes in his only game with College Charles-Lemoyne.
2011-12: Pepin led College-Charles Lemoyne in goals and points in his first season in midget AAA hockey. He scored 22 goals with 18 assists in 38 games and was third on the Riverains with 93 penalty minutes. Pepin was the second player taken in the 2012 QMJHL Entry Draft after Sherbrooke selected Donald Audette — being chosen in the first round by Prince Edward Island.
2012-13: Pepin played in the Quebec Major Junior Hockey league as a 16-year-old and represented Canada Quebec in the 2013 U17 World Hockey Challenge. In 64 regular season games with Prince Edward Island he scored 18 goals with 12 assists and was -9 with 78 penalty minutes. The Rocket finished third in the Maritimes Division; falling to Val d’Or in six games in a first round series. Pepin scored 1 goal with 1 assist and was -2 with 4 penalty minutes in six playoff games. In six games for Canada Quebec at the WHC he scored 3 goals with 4 assists and 18 penalty minutes.
2013-14: Pepin played for Canada’s gold medal U18 team at the 2013 Ivan Hlinka Memorial tournament in August before returning to Charlottetown for his second junior season. After a slow start he was traded to Gatineau in exchange for a player and two first round picks. Pepin scored 8 goals with 9 assists and was -8 with 58 penalty minutes in 37 games with the re-christened Islanders before the trade. In 23 regular season games with Gatineau he scored 9 goals with 8 assists and was +7 with 11 penalty minutes. The Olympiques finished fourth in the West Division and advanced to the second round in the playoffs. Pepin scored 4 goals with 1 assist and was +4 with 4 penalty minutes in eight playoff games. He had no points or penalty minutes in five games at the Ivan Hlinka Tournament. Canada defeated the USA, 4-0, in the gold medal game. Pepin was ranked 110th amongst North American skaters in Central Scouting’s final rankings prior to the 2014 NHL Draft and was invited to the NHL Scouting Combine in May.