In 1994, Duquette returned to Massachusetts to become the General Manager of the Boston Red Sox. He spent eight years at the helm of his hometown team. The Red Sox achieved a record of 656–574 under Duquette, setting attendance records and appearing in the playoffs on three separate occasions (1995, 1998, and 1999). The team won the American League East division in 1995, but only advanced as far as the American League Championship Series once in their three postseason years. They would lose that series to the rival New York Yankees.