The following winter, the Mariners sent him to San Diego for Scott Sanders. Hitchcock is best remembered for his performance in the 1998 playoffs with the Padres, in which he was named the NLCSMVP. He was the winning pitcher in both of his starts with a 0.90 ERA in the NLCS. Overall in the 1998 playoffs he was 3–0, allowing 3 runs in 22 innings (1.23 ERA) with 32 strikeouts.
His successful years with the Padres were followed by struggles with injuries. He underwent Tommy John surgery.[3] The Padres traded Hitchcock back to the Yankees in mid-2001 for two minor leaguers. Hitchcock was the winning pitcher for the Yankees in Game 5 of the 2001 World Series. He re-signed with the Yankees after the season.[4] The Yankees traded Hitchcock to the St. Louis Cardinals in 2003 for Justin Pope and Ben Julianel. He finished his career with the Padres in 2004.
During the regular season, Hitchcock's career-best win–loss record was 13–9 with Seattle in 1996. His career-best ERA was 3.93 with the Padres in 1998.