Schmidt was then acquired by the Giants in 2001 with John Vander Wal in exchange for Armando Ríos and Ryan Vogelsong. Schmidt saw more success in San Francisco. Between his stints in Pittsburgh and San Francisco during the 2001 season, Schmidt compiled thirteen wins. Schmidt re-signed as a free agent with San Francisco that winter, in what would become a five-year $41 million deal. He went on to win thirteen again in 2002 when the Giants made a World Series appearance, but lost to the Anaheim Angels. Schmidt started Games 1 and 5 of the 2002 World Series, picking up the win in Game 1 and a no-decision in Game 5. In 2003, he won 17 games. Schmidt threw a 2–0 shutout in Game 1 of the 2003 NLDS, beating Josh Beckett, but his team lost once again in the playoffs, this time to the Florida Marlins. Schmidt was an All-Star this year as well as the league leader with a 2.34 earned run average. He placed second to Éric Gagné in the 2003 National League Cy Young Award voting.