As a sophomore at Yonsei University, Lee made his first appearance with the South Korea national baseball team in November 1999, at the 1999 Intercontinental Cup held in Sydney, Australia.
The team eventually earned the silver medal, and Lee won home run and batting average titles including All-Star selection.
In November, Lee was called up to the South Korean national team as an amateur player again, and competed in the 2001 Baseball World Cup.
Lee made his first major impact in Game 2 of the 2006 Semi-playoff when he hit a grand slam in the 6th inning, off of Triple Crown winner Ryu Hyun-Jin which gave the Kia Tigers a 6–1 victory over the Hanwha Eagles.
He played in all 137 regular-season games, and posted career highs in batting average (.338), hits (153), runs (63), doubles (31), RBI (48) and walks (43).
Lee stole a career-high 11 bases, but finished the season with the second-lowest career batting average of .253, 2 home runs, 33 RBIs and 92 hits.
On November 14, 2009, Lee belted a pinch-hit RBI double in the ninth off Wirfin Obispo against the Yomiuri Giants at the 2009 KBO-NPB Club Championship.