The 2003 West Coast Conference Baseball Championship Series was held on May 23–25, 2003 at Pepperdine's home field, Eddy D. Field Stadium in Malibu, California, and pitted the winners of the conference's two four-team divisions. The event determined the champion of the West Coast Conference for the 2003 NCAA Division I baseball season. San Diego won the series two games to one over Pepperdine and earned the league's automatic bid to the 2003 NCAA Division I Baseball Tournament.