Signed by the Kia Tigers on January 15,, Lee made his KBO pro league debut on May 2, 2002. In the season, Lee became the regular starter at third base for the Tigers, batting a respectable.263 with 92 hits, 5 home runs and 43 RBI in 129 games. Lee made his first major impact in Game 2 of the 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. Lee's season was the best of his career, thus far. He played in all 137 regular-season games, and posted career highs in batting average, hits, runs, doubles, RBI and walks. Lee won his first batting title, and led the KBO league in hits. In November, Lee was selected again for the South Korea national team, and competed in the 2007 Asian Baseball Championship in Taiwan. However, he had only three at-bats through the tournament, mainly appearing as a pinch runner in the games. Lee faded the following year. His batting average dipped to just.257, batting at the bottom of the order in the 2008 season. Although Lee hit 40 RBIs and again had 100-plus hits, he was considered one of the most disappointing offensive players in the 2008 KBO season. In 2009, Lee played in 120 games as a starting shortstop for the Tigers. However, he struggled at the plate, batting 9th in the order during the whole season, and failed to have three consecutive seasons of 100-plus hits. 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. In the 2009 Korean Series, however, Lee showed his great offensive performance, batting.316 in seven games and smacking a solo home in Game 4, and received a Korean Series champion ring. In 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. Lee played a couple of mediocre seasons as a utility infielder with the Tigers before being released into free agency after the 2012 season.
NC Dinos
Lee was signed by the NC Dinos as a free agent before the 2013 season to a three-year deal. In Dinos franchise debut at home on April 2, 2013, Lee stole the first base in Dinos history in a 4-0 loss to the Lotte Giants. He also hit the franchise's first double off Giants starter Ko Won-Jun and scored its first run in the April 3 contest. In the beginning of the 2013 season, Lee was given a chance to be a starting shortstop. However, he struggled on the plate, hitting.225 with only one RBI through April. In early May, Dinos manager Kim Kyung-Moon installed rookie shortstop No Jin-Hyuk as the starter instead and Lee was benched.