Epstein was born to a secular Jewish family in New York City and raised in Brookline, Massachusetts. He attended Brookline High School (a 1991 graduate), and played baseball for the Brookline High School Warriors, but dreamed of working for the Red Sox. Epstein attended Yale University where he lived at Jonathan Edwards College. He served as sports editor of the Yale Daily News.

On October 12, 2011, Epstein agreed to a five-year contract worth $18.5 million with the Chicago Cubs. On October 19, 2011, it was reported that Epstein's official title with the Cubs would be President and that San Diego Padres general manager Jed Hoyer would take the GM position with the Cubs.  On October 23, 2011, he took out a full-page ad in The Boston Globe, thanking Red Sox fans and the team's owners for their support. Two days later, the Cubs officially introduced Epstein as president of baseball operations. While the Red Sox were already a winning team when Epstein was hired in Boston, the Cubs were coming off a fifth-place finish in the National League Central and had a depleted farm system. The Cubs finished in last place in the National League Central for the first three years of Epstein's presidency, as the focus was to acquire young talent rather than maximize short-term competitiveness. After a three-year, top-to-bottom rebuild, the Cubs clinched a playoff berth in 2015; their first since 2008. They advanced to the National League Championship Series, where they were swept by the New York Mets.  Epstein re-signed with the club on September 28, 2016, with a five-year contract estimated to be worth up to $25million. The Cubs finished the 2016 season with a 103-58 record, the best in the MLB and their best since the 1910 season. In the playoffs, they defeated the San Francisco Giants in the NLDS. The Cubs proceeded to beat the Los Angeles Dodgers in the NLCS, winning their first pennant since the 1945 season and sending them to the World Series. The Cubs then won their first World Series championship since 1908, when they defeated the Cleveland Indians in 7 games, breaking the so-called "Curse of the Billy Goat".

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