In 2005, Honda was selected the Japan U-20 national team for 2005 World Youth Championship. In June 2008, he was selected the Japan national team for 2010 World Cup qualification. At this qualification, he debuted against Bahrain on June 22. In August 2008, he also played for Japan U-23 national team at 2008 Summer Olympics. In 2010, he was selected the Japan for 2010 World Cup. Although his original position is offensive midfielder, he was converted to center forward at 2010 World Cup by manager Takeshi Okada. He played in all 4 matches and scored 2 goals, and Japan qualified to the knockout stage. After the 2010 World Cup, he played many matches as offensive midfielder under manager Alberto Zaccheroni. In 2011, he played at 2011 Asian Cup. Japan won the champions and he was selected MVP award. In 2014, he participated 2014 World Cup. He played all 3 matches and scored 1 goal. In 2015, he also participated 2015 Asian Cup. He played 4 matches and scored 3 goals. Although his opportunity to play decreased from 2017, he was selected Japan for 2018 World Cup. he played 3 matches as substitute midfielder and scored 1 goal. He played 98 games and scored 37 goals for Japan until 2018.