Huberdeau played Midget AAA hockey with the Ste. Eustache Vikings of the Quebec Midget League. He led the league in scoring during the 2008–09 season. After his performance, he was drafted in the first round, 18th overall, in the 2009 Quebec Major Junior Hockey League (QMJHL) Midget draft by the Saint John Sea Dogs. He scored a goal in his first QMJHL game, against the Acadie–Bathurst Titan. Huberdeau was the leading scorer among 16-year-olds in the QMJHL for the 2009–10 season, and scored on all six of his shootout attempts. In January 2010, he was named the QMJHL's scholastic player of the month. The Sea Dogs reached the QMJHL finals during Huberdeau's rookie season.
Prior to the start of the 2010–11 season, Huberdeau was 1 of 33 prospects selected to attend the NHL Research, Development and Orientation Camp in August. The prospects were invited to participate to try out potential rule changes the NHL was considering, and also to be briefed with information on security and professionalism to assist with their future careers in the public eye.
Huberdeau was considered a solid prospect for the 2011 NHL Entry Draft at the start of the 2010–11 QMJHL season, and his strong play helped him move up the rankings. He scored 43 goals and added 62 assists in 67 games for the Sea Dogs. At the end of the 2010–11 season, NHL Central Scouting ranked him third among North American skaters, moving up one spot from the mid-season rankings. Ahead of the NHL draft, Russian-based club Vityaz Chekhov made Huberdeau the fifth overall selection in the 2011 Kontinental Hockey League (KHL) Junior Draft. After being informed of his selection, Huberdeau said, "For sure, I don't want to go there. I didn't talk to anybody about that."

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