Lee attended Duksoo High School in Seoul, South Korea. In 2003, he was selected for the South Korea national junior baseball eam and competed in the 5th Asian Junior Baseball Championship held in Bangkok, Thailand. Lee led his team to the 14-0 mercy rule victory over China in the round robin phase of the competition, going 3-for-5 with 3 RBIs. South Korea eventually won the Championship for the second time by beating Taiwan in the final.
In 2006, Lee batted a career-high .318 (third in the KBO league), and was first in hits (154), second in runs (78) and third in stolen bases (38). He also won his first Golden Glove Award. After the 2006 season, he was selected for the South Korea national baseball team and competed in the Asian Games in Doha, Qatar.
In 2008, Lee had another solid season, batting a respectable .312 with 130 hits and 28 stolen bases, but the team did not reach the postseason.
In August 2008, Lee competed for the South Korea national baseball team in the 2008 Summer Olympics, where they won the gold medal in the baseball tournament. He finished the tournament ranked second in batting average (.481). He was at the plate for 3 of South Korea's 7 runs in their first win against Cuba, delivering a RBI single and hitting into a 2-base error by Norberto González. Lee was 4-for-4 in a 10-1 victory over the Netherlands. In the Gold Medal game, he hit a double off Pedro Luis Lazo to bring in Park Jin-Man for South Korea's final run in a 3-2 win over Cuba.
In March 2009, Lee was called up to the South Korea national baseball team again for the 2009 World Baseball Classic. He went 4-for-18 with one RBI and four runs, sharing the starting center field position with Lee Jong-Wook. After the WBC, Lee was out with an ankle injury for the first three months of the 2009 KBO season, running into the outfield wall during the Tigers' 2009 home opener against the SK Wyverns on April 7. Lee returned from injury in early July, but his batting performance dipped, ending the season with a batting average of .266 and 45 hits.