In January 2007, after being granted a work permit, Lee signed for Premier League club Middlesbrough on an 18-month contract. On 24 February 2007, he made his debut, coming on as an 85th minute substitute for Yakubu in the 2–1 win against Reading. On 29 August 2007, he scored his first goal against Northampton Town in the 2007–08 Football League Cup. On 26 January 2008, he scored his second goal against Mansfield Town in the 2007–08 FA Cup. However, he didn't score during 23 appearances in the Premier League and disappointed English fans. His contract expired at the end of the 2007–08 season and Middlesbrough decided not to extend his contract.
Lee was coach Dick Advocaat's first-choice selection at forward for Korea ahead of the 2006 FIFA World Cup, but a knee injury suffered in a K League match forced him to miss the tournament. On 1 November 2007, Lee was banned from the national team for twelve months after it was revealed that he, along with team captain Lee Woon-jae, teammates Kim Sang-sik and Woo Sung-yong, went on a late night drinking spree with several female employees during the 2007 AFC Asian Cup, in which Korea received third place. Unlike the other members who were involved in this incident, because Lee played for Middlesbrough in England, the KFA could not ban him from his club team matches.