Yamaguchi made his professional debut in 1999 during Shooto - Renaxis 2, against Shuichiro Katsumura. After making his debut, Yamaguchi went on a five fight unbeaten streak. He earned a decision win over Jin Akimoto, a submission win over Ryan Diaz, a TKO win over Baret Yoshida, a draw against Masaru Gokita and a knee KO win over Yoshinobu Ota. These victories entitled win a fight for the inaugural Shooto Featherweight Championship, in a rematch against Jin Akimoto. Yamaguchi won a unanimous decision. After defeating Gildo Lima by an armbar, Yamaguchi was to defend his title against Masahiro Oishi. He lost through a triangle armbar. Yamaguchi would drop down to bantamweight and accumulate a 2-1 record. He was given a chance to win the inaugural Shooto Bantamweight Championship, when he faced Yasuhiro Urushitani. He won a unanimous decision, winning a Shooto title in two different weight classes. This was the first fight where he wore his iconic afro. He beat Hiroaki Yoshioka in a rematch with a knee to the body, and defended his bantamweight title in a rematch against Robson Moura. He went on a four fight winning streak, most notably beating Junji Ikoma, before defending the bantamweight title for the second time against Shinichi Kojima. This would be the beginning of their rivalry. Afterwards he TKO'd Setsu Iguchi and Erikas Suslovas, before rematching Shinichi Kojima. He lost in by way of rear naked choke in the first round. Achiving three wins in his next four fights, he fought Shinichi Kojima for the third time. He lost by way of guillotine choke. Moving to King of the Cage he won the junior flyweight title by defeating Frank Baca with a rear naked choke. He fought Greg Guzman next, but the fight wasn't a title defense, as his opponent missed weight. Returning to Japan, he fought mainly in Vale Tudo Japan. He won three fights, most notably against Yosuke Saruta, lost four and drew twice. He found greater success in Pancrase winning three of his next four fights. Interestingly, all four fights were split decisions. He was then scheduled to fight Ryuichi Miki during Pancrase: 285. He won through a split decision, winning his fourth major career title. He lost the title after dropping a unanimous decision to Senzo Ikeda. He fought once in 2018, losing by way of TKO to Yuya Wakamatsu, and once in 2019, losing a unanimous decision to Toru Ogawa.
