Gwynn started his professional career in the Padres' farm system in Washington, Texas, Hawaii, and Nevada before being brought up to San Diego on July 19, 1982. He debuted against the Philadelphia Phillies' champion hitter Pete Rose, who was so impressed with Gwynn's hitting that he said, "What are you trying to do, catch me after one night?"
During the 1982 and 1983 seasons, Gwynn suffered the first of several injuries that would cause him to miss games during his career. In August 1982 he broke his left wrist while catching a fly ball and then broke his right wrist playing winter baseball in Puerto Rico. By mid-1983, however, he was back with the Padres and finished the season with a .309 average.
In 1984, Gwynn took the first of his National League batting championship titles, with a .351 average and 213 hits. He came in third in voting for the league's Most Valuable Player (MVP), even though the Padres lost the 1984 World Series to the Detroit Tigers.