In baseball, Gwynn was primarily a left fielder and designated hitter (DH) at San Diego State. Gwynn hit .301 in his first season, but said he "stunk defensively". In 1980, Gwynn hit .423 with six home runs and 29 runs batted in (RBI) and was named third-team All-American by "Baseball News". The next season, he was a first-team All-American after batting .416 with 11 home runs and 62 RBI. He also was named a first-team all-WAC outfielder. In his three years, he had a career average of .398 and the team went 146–61–4.