Honda was born in Settsu on June 13, 1986. When he played for Seiryo High School, he joined J1 League club Nagoya Grampus Eight in 2004. He played many matches from 2005. In January 2008, he moved to Dutch Eredivisie club VVV-Venlo. Although the club was relegated to Eerste Divisie in summer 2008, returned to Eredivisie in a year. In January 2010, he moved to Russian Premier League club CSKA Moscow and played many matches. He played 94 matches and scored 20 goals for the club. In January 2014, he moved to Italian Serie A club Milan. Although he played many matches until the 2015/16 season, his opportunity to play decreased in the 2016/17 season. In summer 2017, he moved to Mexican Liga MX club Pachuca. After that, he played for Melbourne Victory (2018-2019), Vitesse (2019) and Botafogo (2020). In February 2021, he signed with Portuguese Primeira Liga club Portimonense. However, Portimonense canceled its contract, since the team was unable to register him.
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.
In August 2018, whilst still a player, Honda became a manager for Cambodia national team.