In 2011, Nakajima was selected the Japan U-17 national team for 2007 U-17 World Cup. 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 left midfielder. On March 23, 2018, he debuted and scored a goal for the Japan national team against Mali. However he was not selected the Japan for 2018 World Cup. After the 2018 World Cup, he became a regular player as left midfielder under new manager Hajime Moriyasu and was given "number 10" shirt for the Japan. In 2019, he played at 2019 Copa América. He played 19 games and scored 5 goals for Japan until 2019.