Kobayashi was born in Fuji on February 19, 1983. After graduating from Shimizu Commercial High School, he joined J1 League club Tokyo Verdy in 2001. He played many matches from 2002 and the club won the champions in the 2004 Emperor's Cup. However the club was relegated to J2 League end of the 2005 season. In 2006, he moved to Omiya Ardija with teammate Yoshiyuki Kobayashi. He played 90 matches and scored 14 goals for Omiya in 3 seasons. In 2009, he moved to Norwegian Tippeligaen club Stabæk. In 2010, he moved to Super League Greece club Iraklis Thessaloniki. In 2011, he returned to Japan and joined Shimizu S-Pulse. He won the 2nd place at the 2012 J.League Cup. In 2013, he moved to Major League Soccer club Vancouver Whitecaps. In 2014, he moved to New England Revolution and played until 2017. From 2018, he played USL Championship club Las Vegas Lights and Birmingham Legion.