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. At SummerSlam 1998, Kai En Tai lost to 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 2000, Funaki once again participated in a hardcore battle royal which was won by the defending champion Steve Blackman.

In 2001, Kai En Tai started participating in dark matches before pay-per-view events such as Royal Rumble 2001 and Judgment Day 2001. After Michinoku left the WWF, Funaki 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 WWF's cruiserweight division.

At Survivor Series 2001, Funaki participated in an "Immunity Battle Royal" which was won by Test. Funaki was drafted to WWE's SmackDown! brand. As part of SmackDown! brand, Funaki wrestled for most of the time on Velocity. At Rebellion 2002, Funaki defeated Crash Holly. At Vengeance 2003, Funaki participated in the APA Invitational Bar Room Brawl which was won by Bradshaw.

On March 4, 2004 episode of SmackDown!, Funaki lost to WWE Cruiserweight Champion at the time 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 WWE 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 his first WWE Cruiserweight Championship. Funaki successfully defended the Cruiserweight 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. At 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 former Cruiserweight champions, 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. Since that time Funaki, would regularly team with Scotty 2 Hotty during episodes of Velocity and SmackDown!. During one such Velocity taping, however, Funaki suffered a 2nd Grade 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.

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 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.

In 2011, Funaki worked a RAW live event in Yokohama, Japan. Funaki was the special referee for a match between Divas Champion Beth Phoenix and Kelly Kelly. After the match, The Miz interrupted Funaki and told him to get out of the ring. Funaki returned in 2013 to guest referee another Divas match between Natalya and Aksana on WWE's tour of Japan.

Funaki made a special appearance in a video as a translator for Kenta's first WWE interview with Renee Young in July 2014 on the WWE App.

On the April 1, 2016 NXT Takeover Dallas special on the WWE Network, Funaki appeared in a backstage segment with Shinsuke Nakamura as he was making his way into the arena. He later appeared at ringside that same night sitting next to Japanese star Kota Ibushi.

Funaki currently provides Japanese language commentary for WWE Pay-Per-Views, beginning with WrestleMania 32.