In April 1999, Endo was selected the Japan U-20 national team for 1999 World Youth Championship. At this tournament, he played all 7 matches as defensive midfielder and Japan won the 2nd place. On November 20, 2002, he debuted for the Japan national team against Argentina. After the debut, he became a regular player. In 2004, he played at 2004 Asian Cup and Japan won the champions. However he lost his position from 2005. In 2006, although he was selected Japan for 2006 World Cup, he could not play in the match.