Lee attended Konkuk University in Seoul and began his professional career at FC Seoul, then known as Anyang LG Cheetahs of K League. He contributed to team’s 2000 K League title and 2001–02 Asian Club Championship runner-up. Lee played for the South Korea national team in the 2002 FIFA World Cup and assisted two winning goals against Portugal and Italy with crosses. He followed Guus Hiddink and teammate Park Ji-sung to PSV Eindhoven after the success in the World Cup.

At PSV, Lee flourished under Hiddink’s guidance and soon established himself in PSV’s first team. Known for his endurance, technique, and ability in both defence and attack, Lee was widely regarded as the best left-back in the Dutch Eredivisie. Lee and his compatriot Park were instrumental in PSV Eindhoven’s run to the 2005 UEFA Champions League semi-final, although, to their disappointment, they were knocked out by AC Milan. Despite PSV’s persistent attempts to keep him, Lee moved to the English club Tottenham Hotspur in August 2005. During his PSV career, Lee scored 1 goal and assisted 13 goals.

At Tottenham, Lee was an immediate hit and earned a spot on the Premier League’s best eleven in his debut week. Tottenham coach Martin Jol, at the time of his signing on 31 August 2005, touted him as “the best left-back in Holland.” His form did however fluctuate in the 2005–06 season, despite being almost ever present in a defence which conceded the fourth lowest number of goals in that season.

In the beginning of 2006–07 season, Lee moved to right full-back due to Benoît Assou-Ekotto’s impressive pre-season performance and an injury to regular right-back Paul Stalteri. Lee then faced increased competition when Tottenham signed French defender Pascal Chimbonda on the final day of the transfer period. Lee also suffered a knee injury and in August 2006, Tottenham offered his rights to A.S. Roma of Italy’s Serie A, but he backed out at the last minute for “personal reasons”. An Italian media report said religion played a part in his decision to reject the transfer offer. On 31 August 2006, Lee held a press conference in Korea and denied that religion was a factor in his decision. He said that moving to Roma would have been great for him in terms of football alone but he decided against it for personal reasons that he would not reveal, despite being pressed for answers by 50 attending reporters.

On 9 August 2007, Tottenham manager Martin Jol announced that Lee would be “fit for selection” in “one or two weeks”. On 18 August 2007, Lee made his first start of the season against Derby County. He continued to play regularly for Tottenham in the 2007-08 season, along with League Cup appearances against Blackpool, Manchester City and Arsenal. He missed the final but earned a medal for his contributions.

On 27 August 2008, Lee transferred to German club Borussia Dortmund for an undisclosed fee. He consistently appeared early in the season and Borussia Dortmund announced that Lee’s contract was extended to Summer 2010 in December but he was benched after vice-captain Dedé recovered from his injury.

On 10 July 2009, Lee signed for Al-Hilal for one million euros for one year, with an option by Al-Hilal to renew for a second year. He made 46 league appearances over a two-year spell at Al-Hilal. After the 2010–11 campaign, he was offered another extension, but refused and decided to leave the Riyadh-based club.

Lee officially signed with Vancouver on 6 December 2011. He scored his first MLS goal for Vancouver on 28 April 2012 off a free kick against the Columbus Crew. Lee was a crucial part to Vancouver’s 2012 season and was played as a right back. He was considered one of their best players on the team that year. Lee was awarded with Vancouver’s 2012 Player of the Year on 21 October 2012 after helping the team become the first Canadian team to reach the MLS Cup Playoffs.

He played his final professional game on 27 October 2013 in Vancouver in 3–0 win against the Colorado Rapids. After scoring the first and eventual game-winning goal, 2013 MLS Golden Boot-winner Camilo Sanvezzo presented Lee with the ball during the goal celebration.