In Cherington's new role, he will report to G.M. Ross Atkins and provide an emphasis on player development.
For the 2015-16 school year, the 42-year-old Cherington had been serving as a professor at Columbia University, where he taught a "leadership in sports" class as part of the university's sports management program.
Cherington is a graduate of Amherst College, and, after spending a season with the Cleveland Indians, worked with the Red Sox in a variety of positions from 1999 to 2015.
From 2011 on, Cherington was the Red Sox' G.M., and he led the team to their World Series win in 2013. As a result, Cherington was named Major League Baseball Executive of the Year by The Sporting News, a distinction only two Red Sox executives had ever received prior.
In 2015, after the Red Sox brought Dave Dombrowski in to serve as president of baseball operations and oversee Cherington, he submitted his resignation.
Now, Cherington will go to a Blue Jays franchise that has done well over the past two seasons, with the team making the postseason in 2015 for the first time since 1993.
At the top of their front office, the Jays have the aforementioned Atkins and President of Baseball Operations Mark Shapiro, both of whom have only been in charge of the club for the 2016 season. Cherington will add to them.