Since Zico took over as the national team manager, Santos was a constant on the left side of the Japanese lineup, as a side back in 4-4-2 formation or midfielder in 3-5-2 formation. At 2004 Asian Cup, he played full time in all 6 matches and Japan won the champions. He was selected to Japan's 2006 World Cup squad in May 2006, providing an assist for Keiji Tamada in a group stage match against his former country Brazil. He played 82 games and scored 7 goals for Japan until 2006.