Kobayashi was born in Higashimurayama on April 24, 1992. He joined J2 League club Tokyo Verdy from their youth team in 2010. He played many matches from 2011. In July 2012, he moved to J1 League club Júbilo Iwata. He did not play many matches and Iwata was relegated to J2 end of the 2013 season. He played many matches from 2014 and Iwata was promoted to J1 end of the 2015 season. In August 2016, he moved to Dutch Eredivisie club Heerenveen. He played for the club in 3 seasons. In September 2019, he signed with Belgian First Division A club Waasland-Beveren. In September 2020, he moved to Qatar Stars League club Al-Khor.