In March 1998, Funaki, along with Mens Teioh and Dick Togo, joined the World Wrestling Federation. Initially, they feuded with Taka Michinoku and defeated him and his partner, Justin Bradshaw in a 3-on-2 handicap match at Over the Edge: In Your House. They lost to Michinoku and The Headbangers at King of the Ring 1998 in a six-man tag team match.
Michinoku eventually turned villainous and joined the group, known as Kaientai. At SummerSlam, Kaientai lost to the Oddities members Kurrgan, Giant Silva and Golga in a handicap match. Over time, the stable turned into a tag team, as in 1999, Teioh and Togo (and manager Yamaguchi-san) were given their releases. Michinoku and Funaki were often used for comedic purposes, often having their pre-match promos dubbed—while Michinoku would "deliver" the majority of dialogue for the duo, Funaki would "respond" strongly with a simple "INDEED".
At WrestleMania 2000, Funaki participated in a 15-minute hardcore battle royal for the Hardcore Championship. Funaki pinned Viscera after a diving shoulder block from Bradshaw, but he was later pinned by Rodney. Hardcore Holly ultimately won the match and became the official champion. At Unforgiven, Funaki once again participated in a hardcore battle royal which was won by the defending champion Steve Blackman.
In 2001, Kaientai started participating in non-televised matches before pay-per-view events such as the Royal Rumble and Judgment Day.
Taka Michinoku left the WWF in the fall of 2001, resulting in Funaki moving to singles competition. At Survivor Series, Funaki participated in an Immunity Battle Royal which was won by Test. In 2002, Funaki moved to the SmackDown! brand after WWF roster was split into two brands. He turned face and found himself as a lower card wrestler and adopted the gimmick of "SmackDown!'s number one announcer", performing backstage interviews between matches, while competing in the cruiserweight division. As part of the SmackDown! brand, Funaki mainly wrestled on Velocity. At Rebellion, Funaki defeated Crash Holly. At Vengeance 2003, Funaki participated in the APA Invitational Bar Room Brawl which was won by Bradshaw.
On the March 4, 2004 episode of SmackDown!, Funaki lost to Cruiserweight Champion Chavo Guerrero in a non-title match. On the March 11 episode of SmackDown!, Funaki participated in an 8-man cruiserweight tag team match teaming with fellow cruiserweights Rey Mysterio, Último Dragón and Billy Kidman against Tajiri, Akio, Sakoda and Jamie Noble. At WrestleMania XX, Funaki participated in a Cruiserweight Open for the Cruiserweight Championship but was pinned by Jamie Noble.
On the December 9 episode of SmackDown!, Funaki won a cruiserweight over the top rope number one contender's battle royal which included Chavo Guerrero, Paul London, Billy Kidman, Akio, Shannon Moore and Nunzio. At Armageddon 2004, Funaki defeated Spike Dudley to win the Cruiserweight Championship. Funaki successfully defended the title against Spike Dudley, Akio and Nunzio. His last successful title defense was against Chavo Guerrero on the February 10, 2005 episode of SmackDown!, notably held in Funaki's birth country, Japan.
Funaki lost the championship to Chavo Guerrero in a six-man Cruiserweight Open match at No Way Out 2005. Before Armageddon 2005, he lost to Jamie Noble in a match on Heat. During an interview with then-Cruiserweight Champion Kid Kash on an episode of SmackDown!, Funaki was assaulted by Kash, who gave him a brainbuster onto the interview platform.
At the 2006 Royal Rumble, Funaki faced Kid Kash in a match for the title, when he was entered into a Cruiserweight Open along with four other cruiserweights, including the champion Kash. Funaki was pinned in this one-fall match by then-Raw superstar Gregory Helms, who won the match and title. At No Way Out 2006, Funaki participated in a nine-man cruiserweight match for the WWE Cruiserweight Championship but Helms retained the title. Following this loss, Funaki would regularly team with Scotty 2 Hotty during episodes of Velocity and SmackDown!. During one such Velocity taping, however, Funaki suffered a concussion, where he was unconscious for just under two minutes. Funaki would resume wrestling later that year, forming a tag team of sorts with Scotty 2 Hotty, which was mainly used to put over debuting wrestlers or tag teams.
Funaki returned to WWE television on February 16, 2007 on SmackDown! in a brawl that involved the other SmackDown! cruiserweights and the then-Cruiserweight Champion Gregory Helms.
At No Way Out 2007, Funaki participated in a Cruiserweight Open match for the WWE Cruiserweight Championship but was pinned by the champion Helms. On the May 18 episode of SmackDown!, Funaki was made short work of by recently returned superstar Mark Henry. On the June 29 episode of SmackDown!, Funaki got a shot at the Cruiserweight title against Cruiserweight Champion Chavo Guerrero and Jamie Noble, but came up short. At The Great American Bash, he participated in a match for the Cruiserweight Championship, which Hornswoggle won. On December 14, on an episode of SmackDown!, he wrestled in a squash match against Edge. He also made a televised appearance on January 4, 2008 episode of SmackDown! where he lost to Chavo Guerrero in a Beat the Clock match.
Funaki legitimately broke his nose at a joint SmackDown/ECW taping in Houston, Texas during a dark match against Vladimir Kozlov.
On October 10, 2008, Funaki revealed his full name to be "Kung Fu Naki" during a backstage segment with R-Truth. This was used as the basis for a gimmick change for Funaki; he then came to the ring dressed in a gi and tweaked his moveset to incorporate theatrical martial arts moves. His first match as Kung Fu Naki saw him scoring a pinfall win over Montel Vontavious Porter (MVP) and Shelton Benjamin in a tag team match with R-Truth. Kung Fu Naki then defeated MVP in a singles match on the November 14, 2008 episode of SmackDown when The Great Khali interfered and distracted MVP. His first loss in the character was against WWE Champion Edge on the December 5, 2008 episode of SmackDown. He was inexplicably absent from WWE action until WrestleMania XXVI, where he took part in the 26-man battle royal match, which was won by Yoshi Tatsu. On April 22, 2010, WWE released Funaki, ending his 12-year stint with the company.
Funaki returned to WWE as a special guest referee during their house shows in Japan in 2011 and 2013.
Funaki made a special appearance in a video as a translator for Kenta's first WWE interview with Renee Young. In September, Funaki returned to NXT to feud with The Ascension alongside Kenta, who was now going by the name Hideo Itami.
Funaki would appear on the WWE Network show, The Edge and Christian Show, introducing the hosts, with his voice dubbed over by Howard Finkel.
On April 1, 2016, at NXT TakeOver: Dallas, Funaki appeared in a backstage segment with Shinsuke Nakamura. Funaki would later appear at ringside sitting next to Kota Ibushi.
Beginning at WrestleMania 32, Funaki became one-half of the Japanese commentary team for all WWE pay-per-view events.
In an exclusive interview for WWE's YouTube channel after the final match of the WWE Mae Young Classic on September 12, 2017, Funaki served as Kairi Sane's interpreter.