In June 1999, Fukunishi was selected the Japan national team for 1999 Copa América. At this competition, on June 29, he debuted against Peru. Although there were few his opportunity to play, he was selected Japan for 2002 World Cup and played 5 minutes as a substitute against Russia. After 2002 World Cup, he became a regular player from 2004. At 2004 Asian Cup, he played all 6 matches and scored 2 goals including first goal in the final. He also played at 2005 Confederations Cup and 2006 World Cup. He played 64 games and scored 7 goals for Japan until 2006.