Upon graduation from Gunsan High School, Lee was drafted by the Ssangbangwool Raiders, which became the SK Wyverns after the 1999 season, in the first round of the 1999 KBO Draft. Lee made his debut in the pro league against the Hanwha Eagles in Gunsan on May 10, 1999. Appearing in 65 games, he finished his rookie year in 1999 with a .258 batting average, 4 home runs and 13 RBIs.
Next season, Lee became a fixture in right field for the SK Wyverns, appearing in 105 games. However, his batting average dipped to .245, stealing a career-low 2 bases.
In 2001, Lee bounced back from the sophomore slump, batting a respectable .280 with 90 hits, 7 home runs, 16 doubles and 9 stolen bases.
From 2002 through 2004, he notched three consecutive seasons batting .300+, and won his first Golden Glove Award in 2004.
Along with his batting accuracy, the strong left-armed Lee, the former power pitcher prospect, is also well known for superb defensive skills in right field, which enable him to collect many outfield assists every season. At the inaugural World Baseball Classic in 2006, his defensive skills drew international attention, making acrobatic catches and outfield assists in the tournament.
In the 2007 KBO season, he missed over 40 regular-season games due to injuries, but batted a career-high .350 with 77 hits in 220 at-bats.
In 2008, Lee was placed on the disabled list again and missed 30 games during the season, but batted .300-plus again (.315) with 102 hits in 324 at-bats, compiling 8 home runs, 53 RBIs and a career-high 12 stolen bases.