On January 27, 2016, WWE officially announced that Nakamura would be taking part in the NXT TakeOver: Dallas event. On January 31, Nakamura was said to be reporting to the WWE Performance Center for training and handling logistical matters regarding his move to the company. On February 2, Nakamura arrived in Pittsburgh, Pennsylvania to undergo pre-contract signing medical tests. On February 22, WWE held a press conference in Tokyo, Japan to officially announce the signing of Nakamura to NXT. On April 1, Nakamura defeated Sami Zayn in his debut match at NXT TakeOver: Dallas in a critically acclaimed match. On the April 13 episode of NXT, Nakamura defeated Tye Dillinger in his NXT television debut. On the May 18 episode of NXT, Nakamura teamed up with Austin Aries to defeat the team of Blake and Murphy.
On the May 25 episode of NXT, Austin Aries declared his intention to become the next NXT Champion, which prompted a response from Nakamura, and NXT General Manager William Regal then scheduled a match between the two on June 8 at NXT TakeOver: The End, which Nakamura won. On the June 15 episode of NXT, Nakamura challenged former NXT Champion Finn Bálor to a match that was accepted and won by Nakamura on the July 13 episode of NXT. On August 20 at NXT TakeOver: Brooklyn II, Nakamura defeated Samoa Joe to win the NXT Championship for the first time. On November 19 at NXT TakeOver: Toronto, Nakamura lost the title to Joe in his first defense, marking his first televised loss in NXT. On the December 28 episode of NXT from Osaka, Japan, Nakamura would regain the NXT Championship from Samoa Joe. On the January 4, 2017 episode of NXT, he successfully defended the championship against Joe in a steel cage match. On January 28 at NXT TakeOver: San Antonio, Nakamura lost the championship to Bobby Roode. In his return match on March 8, Nakamura defeated T.J. Perkins and was put into a rematch to face Roode for the NXT Championship on April 1 at NXT TakeOver: Orlando, but he was unsuccessful in reclaiming the championship. On the April 12 episode of NXT, Nakamura made his final NXT appearance, bidding farewell to the Full Sail University crowd.
On the April 4, 2017 episode of SmackDown Live, the first episode after WrestleMania 33, Nakamura made his main roster debut, interrupting The Miz and Maryse following their promo mocking John Cena and Nikki Bella: this did not spark a feud between Nakamura and Miz, since Miz would be traded to Raw because of the Superstar Shake-up. Nakamura began feuding with Dolph Ziggler, whom he defeated in his televised in-ring debut at Backlash. On the May 23 episode of SmackDown Live, it was announced that Nakamura along with AJ Styles, Baron Corbin, Dolph Ziggler, Kevin Owens and Sami Zayn would compete in the Money in the Bank ladder match at Money in the Bank, during which Corbin attacked him with both a ladder and a camera while making his entrance. Nakamura was checked on by medical staff and carried out of the arena, but he would later return during the match and attack all other participants, only to lose the match when Corbin retrieved the briefcase. This led to a match between the two at Battleground on July 23, where Nakamura defeated Corbin by disqualification after Corbin attacked him with a low blow. Two days later on SmackDown Live, Nakamura defeated Corbin in a rematch to end their feud. On the August 1 episode of SmackDown Live, Nakamura defeated John Cena to earn the right to challenge Jinder Mahal for the WWE Championship on August 20 at SummerSlam, where Nakamura lost following a distraction from The Singh Brothers. On the September 5 episode of SmackDown Live, Nakamura defeated Randy Orton to earn another title shot against Mahal for the title at Hell in a Cell, where he lost again. On the October 31 episode of SmackDown Live, Nakamura defeated Kevin Owens to earn a spot on Team SmackDown at Survivor Series, where he was the first man to be eliminated by Braun Strowman in the 5-on-5 Survivor Series elimination match against Team Raw. On December 17 at Clash of Champions, Nakamura teamed up with Randy Orton in a losing effort against Kevin Owens and Sami Zayn, who retained their jobs with Daniel Bryan and Shane McMahon serving as special guest referees. On the inaugural episode of Mixed Match Challenge on January 16, 2018, Nakamura teamed with Natalya in the Mixed Match Challenge tournament, but the duo was defeated by Finn Bálor and Sasha Banks in the first round.
On January 28 at the Royal Rumble, Nakamura would enter the namesake match at number 14 and go on to win the men's Royal Rumble match after last eliminating Roman Reigns. Immediately afterwards, Nakamura announced that he would challenge AJ Styles for the WWE Championship at WrestleMania 34, where he lost to Styles. After the match, Nakamura turned heel by attacking Styles with a low blow followed by a Kinshasa. On the following episode of SmackDown Live, Nakamura said in an interview that he got "too emotional" and was "sorry" for attacking Styles, but when asked to explain more, he sarcastically said "Sorry, no speak English". Later that night, Nakamura cemented his heel turn by attacking Styles and Daniel Bryan, low blowing Styles twice and striking Bryan in the back of the head with a Kinshasa. Nakamura continued to low blow Styles in the following weeks and it was announced that he would get a rematch for the title at the Greatest Royal Rumble. On the April 24 episode of SmackDown Live, Nakamura debuted a new entrance and theme song. At the Greatest Royal Rumble, Styles and Nakamura fought to a double count-out, with Styles retaining the WWE Championship. As a result, another rematch between Nakamura and Styles was made for Backlash with a no disqualification stipulation added on the May 1 episode of SmackDown Live. At the event on May 6, Nakamura and Styles fought to a no contest after low blowing each other, with Styles again retaining the title. Looking for a decisive winner, SmackDown Commissioner Shane McMahon announced one more rematch between Nakamura and Styles at Money in the Bank. Nakamura was granted the right to choose the stipulation for the match after defeating Styles on the May 15 episode of SmackDown Live, which he revealed the following week, to be a Last Man Standing match after attacking Styles with a Kinshasa and giving him a 10-count. At the event on June 17, Nakamura failed to win the title. Later in June, Nakamura suffered a minor injury after being bitten by a police dog.
On July 3, it was announced that Nakamura would face Jeff Hardy for the United States Championship at Extreme Rules. At the event on July 15, Nakamura executed a low blow and Kinshasa on Hardy to win the championship, marking his first main roster title win. After the match, Nakamura was confronted by the returning Randy Orton, who proceeded to attack Hardy before leaving. Nakamura would successfully defend the title in a rematch against Hardy at SummerSlam. On the August 27 episode of SmackDown Live, Nakamura would later refuse to compete, claiming that the United States of America had been renamed Naka-Merica and that he wouldn't face anyone until he found a worthy opponent.
Nakamura competed in his first match since SummerSlam on the September 11 episode of SmackDown Live, losing to Jeff Hardy via disqualification after interference from Randy Orton. After refusing to defend the United States Championship at the Hell in a Cell pay-per-view, general manager Paige ordered Nakamura to defend the Championship on the September 18 episode of SmackDown Live, which he did so successfully, defeating Rusev. At SmackDown 1000, Nakamura lost to the returning Rey Mysterio in a qualifying match for the WWE World Cup at Crown Jewel. Nakamura would successfully retain the title on the October 30 episode of SmackDown Live against R-Truth and then against Rusev at Crown Jewel. Nakamura lost to Raw's Intercontinental Champion Seth Rollins in an interbrand Champion vs Champion match at Survivor Series. On the December 25 episode of SmackDown Live (taped on December 18), Nakamura lost the United States Championship to Rusev, ending his reign at 156 days. On January 27, 2019, at the Royal Rumble, Nakamura defeated Rusev to win his second United States Championship. Later that night, he participated in the Royal Rumble match entering at #3 but was eliminated by Mustafa Ali.
Two days later on SmackDown Live, Nakamura lost the title to R-Truth. Rusev then confronted Truth and pushed him into a title match, but Truth retained the title. After the match, Nakamura joined forces with Rusev into attacking Truth, starting a alliance between the two. On the Fastlane pre-show, Nakamura and Rusev were defeated by The New Day. At WrestleMania 35, Nakamura and Rusev would compete in a fatal four-way tag team match for the SmackDown Tag Team Championship, but were unsuccessful. The duo returned during the 51-Man Battle Royal at the 2019 Super Showdown, but they were both eliminated during the match.
After a brief absence from television, Nakamura returned on the June 25 episode of SmackDown, interrupting Intercontinental Champion Finn Bálor during a backstage interview, and expressed interest in the championship before walking off. On the July 9 episode of SmackDown, Nakamura defeated Bálor in a non-title match. Five days later on the Extreme Rules pre-show, Nakamura defeated Bálor to capture the Intercontinental Championship for the first time in his career. On July 27, he successfully defended his title against Ali at WWE Smackville. Nakamura later started an alliance with Sami Zayn and defeated The Miz with his help at Clash of Champions to retain his Intercontinental Championship. On the October 18 episode of SmackDown Live, Nakamura retained his championship against Roman Reigns after Baron Corbin interfered, causing the disqualification. At Survivor Series, Nakamura lost to NXT North American Champion Roderick Strong in an inter-brand triple threat match also involving Raw's United States Champion AJ Styles. On the November 29 episode of SmackDown, Nakamura and Zayn formed an alliance with Cesaro, as he and Nakamura unsuccessfully challenged The New Day for the WWE SmackDown Tag Team Championship. Following their loss, Nakamura started a feud with Braun Strowman after he pinned Nakamura in a six-man tag team match on the December 12 episode of SmackDown and in a singles match two weeks later. At the Royal Rumble, Nakamura entered to the Royal Rumble match entering at #11, but was quickly eliminated by WWE Champion Brock Lesnar. On January 31 episode of SmackDown, Nakamura lost the Intercontinental Championship to Strowman, ending his reign at 201 days. At the Elimination Chamber pay-per-view on March 8, Sami Zayn, along with Nakamura and Cesaro, defeated Braun Strowman in 3-on-1 handicap match for the Intercontinental Championship. Zayn became the new champion, pinning Strowman. Nakamura, Zayn and Cesaro then began feuding with Daniel Bryan and Drew Gulak, where Gulak defeated Nakamura to earn Bryan an Intercontinental Championship match against Zayn at WrestleMania 36. At the event, Zayn defeated Bryan to retain the Intercontinental Championship with the help of Nakamura and Cesaro.
Following this, Nakamura began teaming with Cesaro more frequently as they feuded with the New Day for the SmackDown Tag Team Titles. On the July 10 episode of SmackDown, Nakamura and Cesaro challenged the New Day for the SmackDown Tag Team Titles, but the match ended in a no contest with Cesaro and Nakamura putting Kofi Kingston and Big E through a table. On July 19 at The Horror Show at Extreme Rules, Nakamura and Cesaro defeated Kingston and Big E in a tables match to capture the titles, marking Nakamura's first reign. On the October 9 WWE 2020 Draft edition of SmackDown, they lost the titles to The New Day's Kofi Kingston and Xavier Woods. The next Monday on the WWE 2020 Draft edition of Raw, Nakamura and Cesaro were drafted to SmackDown as the nineteenth pick.
On the January 8, 2021 edition of SmackDown, Nakamura competed in a gauntlet match to determine the challenger for the WWE Universal Championship at the Royal Rumble, defeating Rey Mysterio, King Corbin, and Daniel Bryan, the latter of whom he proceeded to shake hands with following Bryan's loss, before losing to Adam Pearce after being assaulted by champion Roman Reigns and Jey Uso, turning face for the first time since 2018. The following week, Nakamura reverted back to his original theme song for his entrance and cemented his face turn by insulting Jey Uso before defeating him in a match. At Fastlane in March, he lost to Seth Rollins. On the May 7 special “Old School” SmackDown episode, he teamed with Kevin Owens, Big E and the Street Profits in a losing effort against the heel team of Sami Zayn, Intercontinental Champion Apollo Crews, the Alpha Academy and the returning King Corbin, after Corbin hit Nakamura with the End of Days for the win. On the final SmackDown before WrestleMania Backlash, he lost to King Corbin in three minutes, when Nakamura locked in an arm bar and Corbin countered by stacking him for the pin. However, post match he kicked the crown off of Corbin and beat him down, stealing his crown in the process. On the June 18 episode of SmackDown, Nakamura would defeat Corbin in a "Battle for The Crown" match to officially become the new King of WWE. Nakamura defeated Corbin on the July 9 episode of SmackDown to qualify for Money in the Bank. At the event, Nakamura failed to win the match. On the August 13 episode of SmackDown, Nakamura defeated Apollo Crews to win the Intercontinental Championship for the second time in his career. On the October 8 episode of SmackDown, just prior to the start of the King of the Ring tournament that night, Nakamura respectfully relinquished the crown. On January 29, 2022, Nakamura entered the Royal Rumble match at the namesake event at number two, but was eliminated by AJ Styles. Nakamura would lose the Intercontinental Championship to Sami Zayn on the February 18 episode of SmackDown.
At WrestleMania 38, Boogs and Nakamura faced The Usos for the SmackDown Tag Team Championship, in which The Usos retained. During the match, Boogs suffered a torn quadriceps/patellar tendon injury, requiring surgery. Subsequently, on the April 8 SmackDown, Nakamura was attacked by newly crowned WWE Universal Champion Roman Reigns and the Usos. On the June 3 episode of SmackDown, he teamed with Riddle to face the Usos for the titles, but lost. Nakamura then failed to qualify for Money in the Bank when he lost to Sami Zayn on the June 24 episode of SmackDown, and in a last chance battle royal on the following episode of Raw. On the August 12 episode of SmackDown, he faced Gunther for the Intercontinental Championship in a losing effort.
On the October 19 edition of NXT, Nakamura returned to the brand for the first time in over five years as Tony D'Angelo's hand-picked opponent against Channing "Stacks" Lorenzo, whom he would end up defeating.
After six months away from WWE programming, Nakamura made his return on the April 14, 2023 episode of SmackDown, defeating Madcap Moss. As part of the 2023 WWE Draft, Nakamura was drafted to the Raw brand. On the May 29 episode of Raw, Nakamura defeated Bronson Reed to qualify for the Money in the Bank ladder match, which was won by Damian Priest. On the August 7 episode of Raw, Nakamura teamed up with Cody Rhodes and World Heavyweight Champion Seth "Freakin" Rollins to defeat The Judgment Day (Finn Bálor, Damian Priest and Dominik Mysterio) in a six-man tag team match. After the match, Nakamura attacked Rollins, thus turning heel for the first time since 2021. At Payback on September 2, Nakamura faced Rollins for the World Heavyweight Championship, but was unsuccessful in winning it. The next month at Fastlane, Nakamura was once again defeated by Rollins with the title on the line, this time in a Last Man Standing match. After his defeat at Fastlane, Alpha Academy's Akira Tozawa engaged in a minor feud between his stable and Nakamura, where Nakamura would defeat Tozawa, Otis, and Chad Gable in successive episodes of Raw. On the November 27 episode of Raw, Nakamura attacked Cody Rhodes, spraying his face with mist. The two would fight on the December 11 episode of Raw, with Rhodes winning by disqualification as Nakamura once again utilized the mist to blind Rhodes. Nakamura would continue to torment Rhodes through promos, including a segmented entitled 'The American Nightmare Before Christmas' on the December 18 episode of Raw, which included Nakamura insulting Rhode's father, Dusty Rhodes, leading to Rhodes attacking him backstage. Finally, on the January 8, 2024 episode of Raw, Nakamura and Rhodes fought in a street fight, with Rhodes defeating Nakamura to end the feud.
Nakamura was an entrant in the 2024 Royal Rumble, where he entered sixth before being eliminated by the eventual winner Cody Rhodes. The two would face off in a bull rope match on the February 5 episode of Raw, where Rhodes would win once again. During the 2024 draft, Nakamura was drafted back to the SmackDown brand. After a six month absence, Nakamura returned on the November 15 episode of SmackDown, attacking LA Knight after his match with Berto.