On May 24, 2008, Nagatomo debuted for the Japan national team against Ivory Coast. He became a regular player as left side back soon. In August 2008, he also played for Japan U-23 national team at 2008 Summer Olympics. In 2010, he was selected the Japan for 2010 World Cup. He played full-time in all 4 matches and Japan qualified to the knockout stage. In 2011, he participated 2011 Asian Cup. He played full-time in all 6 matches and Japan won the champions. He also played at 2013 Confederations Cup, 2014 World Cup and 2015 Asian Cup. In 2018, he was selected the Japan for 2018 World Cup. He played full-time in all 4 matches and Japan qualified to the knockout stage. In 2019, he played at 2019 Asian Cup and Japan won the 2nd place.