He was the manager the team played in the 2006 World Baseball Classic and won every game they played in Pool A. They advanced to round two, again winning all three games to secure a place in the semifinals. Upon reaching the semifinals, the South Korean government announced that it would waive for the players on the team the mandatory two-year military service required of all young Korean men. However, at the semifinals, the Korean team lost to Japan, whom they had beaten twice previously. This led to controversy in Korea over the regulations of the WBC concerning the fact that Korea had to face Japan three times and that it was Japan that was allowed to go to the finals, when it had four victories and three losses up to that point, two of those losses to Korea, while the Korean team, which had only one loss and had already beaten Japan twice, was eliminated from the finals. Kim also led the Korean team to the final of the 2009 World Baseball Classic.