He is best known for his work in New Japan Pro Wrestling (NJPW), where he is a former three-time IWGP Heavyweight Champion, five-time IWGP Intercontinental Champion, one-time IWGP Tag Team Champion and the winner of the 2011 G1 Climax, 2006 G1 Tag League, and 2014 New Japan Cup tournaments. Nakamura is the youngest IWGP Heavyweight Champion in history, having won the title for the first time at the age of 23 years and 9 months. In 2015, Nakamura was inducted into the Wrestling Observer Newsletter Hall of Fame.
In April 2009, Nakamura turned heel, siding with the former members of GBH (especially Toru Yano) in a feud against Togi Makabe and Tomoaki Honma. This new group was soon named Chaos with Nakamura as their leader. Nakamura began to work a much rougher style, using a lot of knees and continuing to use a straight right hand as a frequent move in addition to the Bomaye, his new finisher.
On January 4, 2014, Nakamura lost the IWGP Intercontinental Championship to Hiroshi Tanahashi in the main event of Wrestle Kingdom 8 in Tokyo Dome. A rematch between the two took place on February 9 at The New Beginning in Hiroshima and saw Nakamura fail in his attempt to regain the IWGP Intercontinental Championship.