The 40-year-old Boucher had been GM and vice-president of hockey operations in Rimouski for two years.
He is to be officially introduced as Roy's successor on Monday in Quebec City.
Roy, who remains a co-owner of the Remparts, was recently named head coach and VP of hockey operations of the Colorado Avalanche. The Hall of Fame goaltender had coached and managed the Quebec Major Junior Hockey League club since 2005.
"I realized I'm ready for a new challenge," said Boucher, a defenceman for 16 NHL seasons with Buffalo, Los Angeles, Dallas and Pittsburgh.
He sent a tweet that read: "Goodbye Rimouski, thanks for the memories."
Under Boucher, the Oceanic reached the QMJHL final in 2011-12.
The club had four players selected in the NHL draft on Sunday: defenceman Samuel Morin 11th overall by Philadelphia, forward Frederik Gauthier 21st by Toronto, goalie Philippe Desrosiers 54th by Dallas and defenceman Jan Kostalek 114th by Winnipeg.
The Oceanic announced that head coach Serge Beausoleil will add the GM title to his job and that Alan Johnston will be a full time assistant coach. Owner Maurice Tanguay, 79, is to return to the front office as a special adviser to Beausoleil.