In 2016, Kubo 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. However he could not participate 2016 Summer Olympics because BSC Young Boys deny his dispatch. On November 11, 2016, Kubo debuted for the Japan national team against Oman. He played 13 games and scored 2 goals for Japan until 2018.