Ishii was signed as a free agent by the Los Angeles Dodgers in 2002 after the Dodgers posted the top bid for the right to negotiate with him. He made his major league debut on April 6, 2002, striking out ten batters and allowing two hits and no runs in five and two-thirds innings against the Chicago Cubs. He went on to win his first six starts and was named National League Rookie of the Month for April 2002.
On September 8, 2002, Ishii was struck in the face by a ball hit by Brian Hunter of the Houston Astros. Ishii underwent emergency surgery for a nasal fracture wherein he had bone chips removed and replaced with a small titanium plate. He did not pitch again that season. Ishii led the major leagues with 106 walks but finished with a 14–10 record and placed fourth in National League Rookie of the Year voting.