Bouchard coached AAA midget hockey from 1998 to 2012. He spent four seasons with the Trois-Rivières Estacades as an assistant coach from 1998 to 2002, two seasons as the head coach of the Bois-Francs Cascades Espoir from 2002 to 2004, and eight seasons as head coach of the Trois-Rivières Estacades from 2004 to 2012. He did not pursue coaching at a higher level sooner due to a desire to stay closer to his family, and establish a teaching position in charge of AAA midget and sport studies. Bouchard served as head coach of the UQTR Patriotes for the 2012–13 Canadian Interuniversity Sport season. He successfully rebuilt the Patriotes, and led the team to its first Queen's Cup championship since 2007, with a five-game victory over the Waterloo Warriors.
Rouyn-Noranda Huskies
Bouchard served as head coach and general manager of the Rouyn-Noranda Huskies in the Quebec Major Junior Hockey League for five seasons from 2013–14 to 2017–18. He succeeded André Tourigny for the 2013–14 QMJHL season. Bouchard felt that his background coaching midget hockey helped him quickly adapt to the QMJHL. He led the Huskies to fifth place in the west division, and tenth overall in the regular season. In the playoffs, the Huskies defeated the Quebec Remparts four games to one in the first round, then lost in four games to the Baie-Comeau Drakkar in the second round. In the 2014–15 QMJHL season, Bouchard led the Huskies to fourth place in west division, and eleventh overall in the regular season. The Huskies lost to the Val-d'Or Foreurs in six games in the first round of the playoffs. Bouchard led the Huskies to 113 points in the 2015–16 QMJHL season, winning the Jean Rougeau Trophy as the top team in the QMJHL. In the playoffs, the Huskies defeated the Drummondville Voltigeurs in four games in the first round, defeated the Blainville-Boisbriand Armada in five games in round two, defeated the Moncton Wildcats in six games in round three, then defeated the Shawinigan Cataractes in five games in the finals. The playoff victory was the first President's Cup for the Huskies, and qualified the team for the Memorial Cup. Bouchard was awarded the Maurice Filion Trophy as the QMJHL general manager of the year, and the Ron Lapointe Trophy as the QMHL coach of the year. He was the first person in the league's history to win both awards in the same season. Bouchard led the Huskies to the 2016 Memorial Cup, and defeated the Brandon Wheat Kings by a 5–3 score in game one. The Huskies lost game two to the Red Deer Rebels by a 5–2 score, and lost game three to the London Knights by the same 5–2 score. In the cup semifinals, the Huskies pulled out a 3–1 win over Red Deer to reach the championship game. The Huskies were tied 2–2 with London after regulation time in the Memorial Cup final, but lost in overtime. After the Memorial Cup, Bouchard was awarded the Brian Kilrea Coach of the Year Award as the top overall coach in the Canadian Hockey League. Bouchard led the Huskies to another first-place finish in the west division for the 2016–17 QMJHL season, and second overall in the QMJHL. In the playoffs, the Huskies defeated the Halifax Mooseheads four games to two in the first round, then lost to the Chicoutimi Saguenéens in seven games in round two. In the 2017–18 QMJHL season, the Huskies placed third in the west division and seventh overall in the league, but lost to the Sherbrooke Phoenix in seven games in the first round of the playoffs. During the 2018 playoffs, Bouchard was fined $1,000 by the QMJHL for inappropriate statements to the media, in which he brought an injured played with a bloody nose to a post-game press conference. In five seasons and 340 regular season games, Bouchard won 204 games as head coach of the Huskies.