He traveled to Los Angeles and trained at the local NJPW dojo. He debuted for the promotion in a match against Wataru Inoue at the Korakuen Hall on October 12, 2002. He started out working on the lower card to gain experience. He lost to Ryusuke Taguchi on December 27, 2003 in a chance to compete at the January 4 Dome Show. He defeated Hirooki Goto, Aikya Anzawa, and Hiroshi Nagao in the 2004 Young Lion Cup and earned six points but it was not enough to qualify in the finals. Yamamoto also competed in the 2005 Young Lion Cup where he only won one match when he defeated Yujiro. In 2006, he competed in his first G1 Climax tournament but lost all four matches. He competed and teamed with Manabu Nakanishi in the 2006 G1 Tag League and they defeated Giant Bernard and Travis Tomko to earn their only win in the tournament. During the Summer of 2007, he teamed with Hiroshi Tanahashi in a team called "New Japan Dragons" in a number of matches. Yamamoto and Tanahashi challenged then-champions Bernard and Tomko for the IWGP Tag Team Championship but lost. His last match in NJPW was on November 2, 2007 where he teamed with Yuji Nagata against Tomohiro Ishii and Toru Yano but they lost the match. 