The club has scheduled a news conference for 2:30 p.m. PT Monday at PETCO Park. The team said it will "make a major club announcement" at that time.
Hoyer, 35, will replace Kevin Towers, who was GM for 14 seasons before new Padres chief executive Jeff Moorad informed him near the end of the season that he would not be retained for 2010.
Hoyer will take over a young squad that went 33-25 during the last two months of the season, before finishing with a 75-87 record to take fourth place in the National League West in 2009.
Hoyer has spent his entire front-office career with the Red Sox, starting in 2002 as a baseball operations intern and becoming a baseball operations assistant the following year. Hoyer and Ben Cherington served briefly as co-GMs after the 2005 season when Theo Epstein was working through contract issues.
Hoyer interviewed for the Pirates' GM job in 2007, declined an interview with the Mariners in 2008, and interviewed for the Nationals' GM job this year.
A Plymouth, N.H., native, Hoyer played shortstop and pitched at Wesleyan University, and was an assistant coach at the school for two years. Hoyer's background in quantitative analysis was part of what Moorad sought in a GM.
This is the second time Moorad has hired a GM who had worked under Epstein in Boston. As CEO of the Arizona Diamondbacks, Moorad signed Josh Byrnes as GM in October 2005 to replace Joe Garagiola Jr. Under Byrnes, the D-backs won the National League West by a half-game in 2007, lost the division by two games in 2008 and, under the weight of injuries and underperformance, lost 92 games this season.
Moorad left the D-backs earlier this year, and he and his group purchased 33 percent of the Padres from principal owner John Moores just prior to the start of the season. Moorad's group plans to continue buying out Moores over the next four years.
Hoyer will become only the third Padres GM since Moores bought the club after the strike-shortened 1994 season, following Towers and Randy Smith, who returned to the organization as director of international scouting.
Though Hoyer's background is in quantitative analysis, he has become more schooled in the ways of Major League transactions, contracts, scouting and player development, essentially making him the hybrid candidate who can balance statistical analysis with a scouting background.
As we see it, we want every piece of information possible before making a decision," Hoyer said in a 2007 interview with Baseball Analysts. "We have spent a lot of time and energy in developing our quantitative methods, and we certainly use them in making player-personnel decisions.
"But we also have a lot of great scouts, and we read their reports and have lengthy conversations with all of them before making decisions. The idea that teams are either 'Moneyball' teams or 'scouting' teams is an incredible oversimplification. You need to have both of those components -- as well as medical and contractual -- to make an educated decision on a player."
Hoyer will take over a club that has its manager and coaching staff in place. This past week the club announced that manager Bud Black has invited his entire coaching staff back for next season. The only uncertainty is hitting coach Randy Ready, who has interviewed for the Astros' managerial job. He's invited back if the Astros do not hire him.
The other coaches are bench coach Ted Simmons, pitching coach Darren Balsley, first base coach Rick Renteria, third base coach Glenn Hoffman and bullpen coach Darrel Akerfelds.
On Aug. 7, Black agreed to an extension through 2010, with a club option for 2011.
Thomas Harding is a reporter for MLB.com. Barry M. Bloom contributed to this report. This story was not subject to the approval of Major League Baseball or its clubs.