Lountzis was the captain of the junior Greek Under-16 national team at the 2014 FIBA Europe Under-16 Championship. He also played with Greece's junior national teams at the 2015 FIBA Under-19 World Cup, the 2015 FIBA Europe Under-18 Championship, where he won a gold medal, and at the 2nd division 2016 FIBA Europe Under-20 Championship Division B, where he won a bronze medal. He also played at the 2017 FIBA Europe Under-20 Championship, where he won a gold medal.