Honda was born in Sagamihara on April 17, 1985. After graduating from Hosei University, he joined J1 League club Shimizu S-Pulse in 2008. He played many matches as defensive midfielder from first season. Shimizu won the 2nd place in the 2008 J.League Cup and 2010 Emperor's Cup. In 2011, he moved to Kashima Antlers. However he could not play many matches for injury. In July 2013, he returned to Shimizu S-Pulse. Although he played many matches, Shimizu was relegated to J2 League first time in the club history end of the 2015 seasons. In 2017, he moved to Montedio Yamagata and played in 4 seasons. In 2021, he moved to J3 League club FC Gifu.