In 2007, Havenaar was selected the Japan U-20 national team for 2007 U-20 World Cup. In 2011, he was selected the Japan national team for 2014 World Cup qualification. At this qualification, he debuted against North Korea on September 2. He also played at 2013 Confederations Cup. He played 18 games and scored 4 goals for Japan until 2016.