In February 2007, Lee obtained Japanese citizenship. In 2008, he was selected the Japan U-23 national team for 2008 Summer Olympics and played all 3 matches. In January 2011, he was selected the Japan national team for 2011 Asian Cup. At this tournament, he debuted against Jordan on January 9. His first international goal was dramatic, coming as it did in the 109th minute of the final to secure a 1–0 win over Australia and Japan on the champions. He played 11 games and scored 2 goals for Japan until 2012.