After the Noah secession, he joined the upstart promotion and became an integral part of its Junior Heavyweight division, impressing many with his high-flying style and charisma.

On September 9, 2006, Naomichi defeated Jun Akiyama for the GHC Heavyweight Championship at the Budokan Hall, utilizing the Perfect Inside Cradle.

[10] That same night, Maybach Taniguchi won a number one contenders match over Nakajima and the two men squared off on September 23 at the 'Great Voyage in Niigata' show where Marufuji successfully retained his championship.

[11] Shortly after, he retained the championship for a fourth time by defeating Daisuke Sekimoto of Big Japan Pro Wrestling at the 'Great Voyage in Yokohama' show on October 23.

[17] In the final, Marufuji defeated fellow Suzuki-gun member Shelton Benjamin who had finished his block without a single loss to go on and receive a championship opportunity.

[19] However, immediately following the match as his Noah roster members celebrated with him, Takashi Sugiura turned on Marufuji to join forces with Suzuki-gun.

[21] On March 19, 2016, Marufuji continued to battle against the Suzuki-gun stable that had invaded Noah as he alongside Muhammad Yone and Mitsuhiro Kitamiya defeated Shelton Benjamin, Takashi Iizuka, and Suzuki himself in a six-man tag team match the 2016 'Great Voyage In Korakuen' event.

[33] On the first show of 2017 on January 7, Marufuji and partner Atsushi Kotoge failed to dethrone GHC Tag Team Champions Go Shiozaki and Maybach Taniguchi in a championship opportunity.

[36] The team took part in the tag league finishing at the top of the block with ten points and ultimately won the final as well by defeating Shiozaki and Kotoge.

[37] The champion duo was then promptly challenged by a team they lost to in the tournament, Cody Hall and Randy Reign, and on June 4 Marufuji and Taniguchi defeated them in a championship title defense.

[39] On December 22, the two received their rematch for the titles, but lost to 50FP (Quiet Storm and Mohammad Yone) after Taniguchi turned on him, revealing himself as the traitor within NOAH that Mitsuya Nagai had been hinting at for several shows.

[42] On May 3, 2004, Marufuji would make his final appearance for NJPW in over five years in a six-man tag team match, where he, Heat and Tiger Mask were defeated by the American Dragon, Koji Kanemoto, and Último Dragón.

[49] After a slow start, which saw Marufuji lose two of his first three matches, he bounced back by defeating reigning IWGP Heavyweight Champion Hiroshi Tanahashi on August 5 and afterward made a challenge for his title.

[56] Marufuji returned to New Japan on December 20, 2014, when he, along with fellow Noah wrestlers TMDK (Mikey Nicholls and Shane Haste), was revealed as one of Toru Yano's tag team partners at Wrestle Kingdom 9 in Tokyo Dome on January 4, 2015.

[57] At the event, the four defeated Suzuki-gun (Davey Boy Smith Jr., Lance Archer, Shelton X Benjamin and Takashi Iizuka) in an eight-man tag team match.

[58] Marufuji returned to NJPW on July 18, 2016, by entering the 2016 G1 Climax tournament and defeating reigning IWGP Heavyweight Champion Kazuchika Okada in his opening match.

[60] As part of his foreign excursion to the United States, Marufuji challenged Bryan Danielson for the ROH World Championship on December 17, 2005, in Edison, New Jersey.

On September 28, 2008, ten years after his original debut in All Japan Pro Wrestling, Marufuji returned to AJPW and won the World Junior Heavyweight Championship from Ryuji Hijikata.

He would go on to successfully defend the title against Shuji Kondo in a match that won the Tokyo Sports Best Bout of 2008 award and Takashi Okita before losing it to Kaz Hayashi.

Marufuji returned to AJPW to compete in the 2018 Champion Carnival, where he finished his block with a record of five wins and two losses to advance to the finals.