In November 1989, Peña was granted free agency and signed a contract to play for the Boston Red Sox. With the Red Sox in 1990, he led American League catchers in games played, range factor, putouts and finished second in assists and in fielding percentage. His performance earned him the Gold Glove Award, making him only the second catcher after Bob Boone to earn a Gold Glove in both the American and National Leagues. The Red Sox won the American League Eastern Division pennant before eventually losing to the Oakland Athletics in the 1990 American League Championship Series.