Aoki has his MMA debut for DEEP in November 2003, winning a one night tournament by fast armbar submissions. He later would show further unorthodox grappling skills against veteran Seichi Ikemoto and Keith Wisniewski, who he defeated by breaking his arm with a standing wakigatame. He also would face legendary Hayato Sakurai in a Shooto event, losing a decision which was seen as controversial. Aoki went to compete in both companies until 2007, also defeating Akira Kikuchi to win the Shooto Welterweight Championship.

In August 2006, Aoki made his PRIDE Fighting Championships debut at Pride Bushido 12, submitting American fighter Jason Black in under two minutes with a triangle choke. Following that win, Aoki was booked to face rising Lightweight star Gilbert Melendez at the following Bushido card, Bushido 13. However, prior to the fight Melendez received an elbow injury (a burst bursa sac) in training and was forced to pull out of the fight. Aoki’s opponent was changed to Clay French. Aoki submitted French in just under four minutes with a triangle choke. Afterwards, Melendez was shown in the crowd with a sling, and announced he would like to face Aoki at Pride Shockwave 2006 on New Year’s Eve. Aoki agreed.

On November 21, 2007, Aoki’s participation on the New Year’s Eve MMA card Yarennoka! was announced. Originally, his opponent was to be two-time K-1 Hero’s Middleweight Grand Prix champion Gesias “JZ Calvan” Cavalcante. Rumors that Cavalcante was injured surfaced only two weeks before the bout, though Cavalcante denied them before eventually admitting the injury and withdrawing from the fight. Aoki defeated Korean Olympic Judo silver medalist Jung Bu-Kyung, Cavalcante’s replacement, via unanimous decision in what was Jung Bu-Kyung’s mixed martial arts debut. Aoki had promised to use a never before seen submission in the match but was unable to finish the debut fighter.

After the purchase of Pride by Zuffa LLC, most Japanese fighters signed to newly created mixed martial arts promotions, with Aoki signing to Dream. Here Aoki finally faced Cavalcante on March 15, 2008 at the opening round of the Dream Lightweight Grand Prix tournament. Early in the first round, the referee stopped the action when Cavalcante apparently landed illegal elbow strikes to the back of Aoki’s neck. The ringside doctor announced that Aoki was unable to continue due to the injury and Cavalcante apologized for the incident. The fight resulted in a no contest. Elbow strikes to the neck and spine area are illegal under Dream rules. Aoki was later found to have sustained concussion of the cervical vertebra.

They had their rematch at Dream 2 on April 29, 2008. In that match, Aoki defeated Cavalcante via unanimous decision. He sustained a severely bruised rib and tore cartilage in his costal area during the match. At Dream 4, Aoki defeated Katsuhiko Nagata via a mounted gogoplata (possibly the first ever in professional competition, later to be dubbed “the Aoki-plata”) submission to advance to the semi-finals of the Dream Lightweight Grand Prix. At Dream 5, Aoki defeated Caol Uno by unanimous decision. Later that night, Eddie Alvarez was set to fight Aoki, but had to bow out due to injury from his previous match that evening. Joachim Hansen took his place and defeated Aoki by TKO (punches) at 4:19 round 1 to become the first Dream Lightweight Champion.

At Dynamite!! 2008 on New Year’s Eve, Aoki finally squared off against American Eddie Alvarez for the WAMMA Lightweight Championship. Aoki started quickly, securing Alvarez’s back after catching a kick, before being thrown to the canvas by the stronger American. In a scramble, Aoki latched onto the foot of Alvarez and applied a heel hook. Alvarez fought the hold, but tapped out shortly after Aoki adjusted his grip. Alvarez also suffered ligament damage in his knee.

Aoki defeated David Gardner at the March 8, 2009 Featherweight Grand Prix card at Dream 7 at the Saitama Super Arena in Saitama, Japan (this fight is remembered for Gardner waving to the crowd as Aoki was controlling his back and saying “Hello, Japan!”, thus allowing Aoki to secure a rear-naked choke from that position). Aoki, who is still recognized by Shooto as its Welterweight (168 pounds (76 kg)) Champion, also moved back to that weight to fight in Dream’s Welterweight Grand Prix at Dream 8 in 2009. His first match in the tournament was a rematch with Hayato Sakurai. Aoki lost the fight in twenty-seven seconds via TKO due to punches and knees following a Sakurai reversal from a takedown by Aoki. As a result of the match, Aoki did not advance in the DREAM 2009 Welterweight Grand Prix.

Aoki defeated Vítor Ribeiro at Dream 10 on July 20, 2009, which earned him a title fight against Joachim Hansen. Aoki faced Joachim Hansen in a rematch for the DREAM Lightweight Championship at Dream 11 on October 6, 2009. Last time they met, Aoki previously fought a tough match against Caol Uno on the same night which went on for both two rounds (15 minutes) when Hansen only fought for 2 minutes 35 seconds previously. Aoki ended up defeating Hansen in the second round for the title shot via submission (armbar) to become the new DREAM Lightweight Champion.

On December 22, 2009, it was announced that Aoki would not be taking on fellow DREAM fighter Tatsuya Kawajiri, but would be fighting Sengoku Lightweight Champion, Mizuto Hirota. In his pre-fight interview Aoki stated that he felt insulted with the short notice changes as he was looking forward to battling it out with one of the world’s other top lightweight competitors in Kawajiri. Aoki’s opponent Hirota just came off a spectacular win over longtime friend of Aoki’s, Satoru Kitaoka to become the new Sengoku Lightweight champion. The fight between Aoki and Hirota was considered to be one of the main events of the night along with Satoshi Ishii vs. Hidehiko Yoshida and the K-1 bout Masato vs Andy Souwer. Aoki defeated Hirota with a brutal submission (hammerlock) that broke Hirota’s arm in the first round at 1:17. He then proceeded to get in the face of his downed opponent and give him the finger then, get up and run around the ring doing the same to the crowd before leaving the ring.

Aoki has received criticisms by the mixed martial arts community for his disrespectful victory celebrations and perceived lack of care for his opponents, often causing injuries which are seen as needless. He firstly became known for breaking Keith Wisniewski’s arm by waki-gatame, then doing the same with Kuniyoshi Hironaka via flying armbar in a Brazilian jiu-jitsu bout, sidelining him for a year. In 2009, controversy would come when he faced Mizuto Hirota in a super bout. After Aoki won by breaking Hirota’s arm in a brutal fashion, he gave the middle finger to the downed fighter and the crowd while running excitedly.

Aoki lost his US debut against then Strikeforce Lightweight Champion Gilbert Melendez on April 17, 2010 at Strikeforce: Nashville. The fight was broadcast live to a North American audience on CBS. After Aoki’s defeat to Gilbert Melendez in Strikeforce he has expressed interest to train at Cesar Gracie’s camp in northern California.

Aoki successfully defended his Lightweight title against top contender Tatsuya Kawajiri in just under two minutes of the first round via an Achilles lock submission, at Dream 15 on July 10, 2010.

Aoki defeated Marcus Aurélio by unanimous decision in a non-title bout on September 25, 2010 at Dream 16.

Aoki then defeated Lyle Beerbohm on April 9, 2011 at Strikeforce: Diaz vs. Daley via neck crank in the first round.

Aoki was expected to face Willamy Freire on May 29, 2011 at Dream: Fight for Japan!. Freire reportedly had trouble getting a visa, and it then appeared that he would be facing Antonio McKee instead, but then McKee chose to pull out of the card. It was then announced that Shane Nelson would fight Aoki, but he was quickly replaced with Rich Clementi. Aoki defeated Clementi by way of Neck Crank/Rear Naked Choke at the 2:32 mark of the second round.

Aoki Took on former Maximum Fighting Championship Lightweight Champion, Antonio McKee at Dream 18 on December 31, 2012. He won via TKO in the second round.

Aoki faced Kotetsu Boku at ONE Fighting Championship: Kings and Champions on April 5, 2013 for the Lightweight Championship. He stated that win or lose, he will be dropping to the Featherweight division after the fight. Aoki defeated his opponent at 2:01 of the second round via rear-naked choke, successfully avenging his Evolve teammate Zorobabel Moreira.

Aoki made his featherweight debut on October 18, 2013 at ONE FC: Total Domination when he took on Cody Stevens. He won the fight via unanimous decision.

Aoki later returned to lightweight and picked up a victory in the Inoki Bom-Ba-Ye promotion before successfully defending his ONE Lightweight Championship against Kamal Shalorus by submission in the first round at ONE FC: Reign of Champions on August 29, 2014.

Aoki began dabbling in pro wrestling in 2014 for Antonio Inoki’s Inoki Genome Federation (IGF), competing in a series of MMA fights on his cards before eventually transitioning to pro wrestling. In 2017, Aoki was announced as a member of Next Exciting Wrestling (NEW), a new show under the IGF banner. Aoki competed on the first show, defeating Keisuke Okuda. Aoki competed for NEW until IGF announced its cancellation in July 2017. In his last match for NEW, Aoki lost to Tatsuhito Takaiwa.

In 2014, after submitting Yuki Yamamoto, Aoki again taunted his opponent and the crowd with a middle finger, while Yamamoto had to be restrained by his cornermen. Shinya left the arena without putting down the taunt.

Aoki defended his title against Koji Ando at ONE Championship 28: Warrior’s Quest on May 22, 2015.

Rizin Fighting Federation announced Aoki would compete on December 29, 2015 against Kazushi Sakuraba in the main event of their inaugural event. He won the fight via TKO at 5:56 in the first round after Sakuraba’s corner threw in the towel.

In the third defense of his title, Aoki faced Eduard Folayang at ONE Championship: Defending Honor on November 11, 2016 in Singapore. He lost the bout and title via TKO in the third round.

Aoki faced Ben Askren on November 24, 2017. He lost the fight via TKO in the fight’s opening minute.

Aoki faced Ev Ting on October 6, 2018 at ONE Championship: Kingdom of Heroes and won the fight via arm-triangle choke in the opening minute of the bout. Due to the victory, Aoki secured a fight for the vacant lightweight championship against the winner of Eduard Folayang and Amir Khan in the promotion’s inaugural event in Tokyo, Japan on March 31, 2019.

After a short hiatus, Aoki announced his return to pro wrestling in 2018, and that he would be competing for DDT Pro Wrestling. Aoki made his in-ring debut at Maji Manji #15, quickly defeating Gota Ihashi. On October 28, at Maji Manji #21, Aoki defeated Harashima to win the DDT Extreme Division Championship. Aoki lost the title back to Harashima on February 19, 2019 at DDT Judgement 2019.

On March 31, 2019 at ONE Championship: A New Era Aoki recaptured the lightweight title in a rematch with Eduard Folayang by defeating Folayang via technical submission.

Aoki lost the title in his first defense against Christian Lee at ONE Championship: Enter the Dragon on May 17, 2019.

Aoki next faced Kimihiro Eto at Road to One 3: Tokyo Fight Night on September 10, 2020. He won the fight via unanimous decision.