The 37-year-old Cherington will also serve as the team's executive vice president.
"Ben Cherington is one of the youngest 'veterans' in the game of baseball," Red Sox president Larry Lucchino in a statement. "He has already worked his way through every aspect of baseball operations, and over the years has gained a well-rounded set of experiences that will help him guide this franchise to its next World Championship. There is no one more prepared to take on the role of general manager of the Red Sox than Ben. He will hit the ground running, in full stride, and no one will outwork him."
A New Hampshire native, Cherington joined the Red Sox organization in 1999 after beginning his career a year earlier with the Cleveland Indians as an advance scout. He had been Boston's senior vice president and assistant GM since January 2009 and also served as a scout, assistant director of player development and vice president of player personnel.
Additionally, Cherington was co-general manager, along with Jed Hoyer, from December 12, 2005 through January 19, 2006 when Epstein briefly left the Red Sox before deciding to return.
Epstein had spent the past 10 seasons with Boston, including the last nine as general manager. Under Epstein, the Red Sox won two World Series (2004, 2007) and reached the playoffs six times.