After 1998 World Cup, in October 1998, Kubo was selected Japan national team by new manager Philippe Troussier. On October 28, he debuted for Japan against Egypt. Although he played at 2000 Asian Cup and 2001 Confederations Cup, his opportunity to play in the matches was few and he was not selected Japan for 2002 World Cup. After 2002 World Cup, in December 2003, he was selected Japan for 2003 East Asian Football Championship and he scored 2 goals against China. This goals were his first goal for Japan. In the first half of 2004, he played as striker and scored 6 goals in 9 games. However, he did not play for low back pain from late 2004. From February 2006, he came back to Japan and he scored 3 goals in 6 matches, however he was not selected Japan for 2006 World Cup. He played 32 games and scored 11 goals for Japan until 2006.