In May 2017, at the age of 15, Kubo was selected the Japan U-20 national team for 2017 U-20 World Cup. In October 2017, he also played for the Japan U-17 national team for 2017 U-17 World Cup. On June 9, 2019, he debuted for the Japan national team against El Salvador. He also participated 2019 Copa América.