In December 2013, Gwynn signed a minor league contract with the Philadelphia Phillies containing an invitation to Major League spring training. At the end of spring training, it was announced that Gwynn had made the opening day roster to start the 2014 season, which culminated a "long road" back to the major leagues. He was the Phillies' opening day starter in left field (Domonic Brown, the projected starter in left field, started at designated hitter as the Phillies opened the season on the road against the Texas Rangers), and batted in the ninth position. Later, when Ben Revere had sore ribs, Gwynn started and batted in the leadoff position, and because of his performance, started several games after Revere had recovered. Following the death of his father, Gwynn Jr. was placed on the bereavement list on June 16, 2014. He was designated for assignment on July 21, 2014, and released on July 28. He later signed a minor league contract with the Phillies on August 3 with an assignment to their Triple-A affiliate, the Lehigh Valley IronPigs. He was called back up by the Phillies on September 2, 2014. On October 10, 2014 he refused assignment to Triple-A and was released.