In July 2015, Endo was selected the Japan national team for 2015 East Asian Cup. At this tournament, he debuted against North Korea on August 2. In 2016, he played for the Japan U-23 national team at 2016 AFC U-23 Championship. Japan won the champions and qualified for the 2016 Summer Olympics. At 2016 Summer Olympics, he played all 3 matches as defensive midfielder. In 2018, he was selected the Japan for 2018 World Cup, but he did not play in the match. In 2019, he participated 2019 Asian Cup. He played 5 matches and Japan won the 2nd place.