On June 18, 2000, Miyamoto debuted for Japan national team against Bolivia. As a center back, he served as captain for Japan in the 2002 World Cup, after an injury to Ryuzo Morioka, who had begun the tournament as captain. He then continued to captain his country through the 2004 Asian Cup and the 2006 World Cup. At 2004 Asian Cup, he played full-time in all 6 matches and Japan won the champions. At 2006 World Cup, he played the first two group matches of the cup, but was suspended for the third and last match against Brazil after he received yellow cards against Australia and Croatia. Yuji Nakazawa wore the armband in his place. This competition was his last game for Japan. He played 71 games and scored 3 goals for Japan until 2006.