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.