Nagata was born in Shizuoka on April 6, 1983. After graduating from Shizuoka Gakuen High School, he joined J1 League club Kashiwa Reysol in 2002. He debuted in September 2002 and became a regular center back in 2003. However he injured his anterior cruciate ligament in March 2005. Although he came back in November, Reysol was relegated to J2 League end of the 2005 season. In 2006, Nagata moved to J1 club Albirex Niigata with teammate Kisho Yano. However Nagata could not play at all in the match for injuries in 2006. He became a regular player in 2007 and played many matches as center back with Mitsuru Chiyotanda (2007-2009) and Kazuhiko Chiba (2010). In 2011, Nagata moved to Urawa Reds with teammate Márcio Richardes. He became a regular center back from first season. However he could not play many matches for repeated injuries from 2013. In 2017, he moved to J2 club Tokyo Verdy. Although he played for the club in 2 seasons, he could hardly play in the match and resigned end of 2018 season. In May 2019, he joined Regional Leagues club Tokyo United FC. He retired end of the 2019 season.