On May 31, 2003, Okubo debuted for the Japan national team against South Korea. He played many matches as forward including 2003 Confederations Cup under manager Zico. He was also selected Japan U-23 national team for 2004 Summer Olympics. He played all 3 matches and scored 2 goals. However he could hardly play in the match in senior team from 2004 and he was not selected Japan for 2006 World Cup. From 2008, he played many matches as offensive midfielder under manager Takeshi Okada. In 2010, he was selected Japan for 2010 World Cup. He played as left midfielder in all 4 matches and Japan qualified to the knockout stage. He also played at 2014 World Cup. He played 60 games and scored 6 goals for Japan until 2014.