Training in judo since chilhood, Aoki became a successful judoka and competed in national and international championships. However, interested in modalities like kosen judo which were away from him due to the Kodokan competition rules, he moved to other combat sports, until landing in mixed martial arts. Aoki initially joined the judo-based RJJ gym before moving to Team Roken along with his longtime friend Masakazu Imanari, though he later moved to Paraestra Shooto Gym, where he trained under former kosen representative Yuki Nakai. He earned both his A-class Shoot wrestler's rank (better known in the West as Catch wrestling) as well as his Brazilian jiu-jitsu black belt under Nakai, and became one of the team's main teachers.
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.
For unknown reasons, the proposed fight with Melendez did not take place. Instead, Aoki faced highly ranked Lightweight fighter Joachim Hansen. Aoki submitted Hansen with a gogoplata—this was the second successful gogoplata in MMA competition (the first by Ryusuke Uemura).
After his win over Hansen, Aoki was set to rematch Kikuchi in Shooto, with Aoki's Shooto Welterweight title (previously won from Kikuchi) on the line. Aoki successfully defended his title against Kikuchi, winning via split decision.
Following his victory, Aoki announced that he was to be the Shooto representative in the forthcoming Pride Lightweight Grand Prix tournament. Aoki's next fight was at Pride 34, where he faced little known Dutch fighter Brian Lo-A-Njoe. At the event Aoki submitted Lo-A-Njoe in the first round with an armbar. Following the fight, Aoki once again confirmed his participation in the Lightweight Grand Prix. With the purchase of Pride by the majority owners of Zuffa LLC, the Pride Lightweight Grand Prix was cancelled.
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 met Fedor Emelianenko during a five-minute "special exhibition" at an April 29 M-1 Challenge (presented by Affliction) event in Tokyo. Emelianenko made Aoki tap out from an Achilles lock.
Aoki defeated Vitor 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 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.
He then competed again at Deep: 50th Impact on October 24 against former PABA and WBA boxing champion Yokthai Sithoar. Aoki won by submission (americana) 1:00 into the first round against Sithoar.
After the proposed rematch with Melendez fell through due to contract issues on Melendez's part, Aoki faced K-1 kickboxer Yuichiro "Jienotsu" Nagashima in a special rules exhibition bout at Dynamite!! 2010. In the first 3-minute kickboxing round, Aoki evaded Nagashima's offense by breaking the rules via excessive clinching, falling to the ground, and going for takedowns in order to run out the clock and move onto the 5-minute mixed martial arts round. Aoki was warned repeatedly by the referee, however no points were deducted as there could not be a decision winner. The commentary team of Michael Schiavello and Frank Trigg were openly criticising Aoki for his rule breaking during the first round, while the Japanese crowd uncharacteristically booed him. At 0:04 of the second MMA rules round, Aoki was knocked out immediately as he went for a double leg takedown via flying knee and subsequent grounded strikes. Since the bout was contested as an exhibition, the loss is not reflected on Aoki's professional mixed martial arts record.
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 minutes mark of the second round.
Aoki defeated Rob McCullough by neck crank at 4:57 of Round 1 at Dream 17.
Aoki fought Satoru Kitaoka for the DREAM lightweight title at Fight For Japan: Genki Desu Ka Omisoka 2011. He won the fight via unanimous decision.
Aoki Took on former Maximum Fighting Championship Lightwight Champion, Antonio McKee at Dream 18 on December 31, 2012. He won via 2nd round tko.
Aoki faced Eddie Alvarez in a rematch at Bellator 66. He lost the fight via TKO in the first round.
On June 27 it was revealed that Aoki had signed an exclusive contract with ONE Championship and would be making his debut at ONE Fighting Championship: Pride of a Nation in Manila on August 31. On August 16 it was revealed that Aoki would be fighting Arnaud Lepont in a lightweight super fight in the main event at ONE Fighting Championship: Rise of Kings He won the fight via triangle choke at 1:25 of round 1.
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 round 2 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 defended his title against Koji Ando at ONE Championship 28: Warrior's Quest on May 22, 2015.
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.
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.
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, 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.
"When I had his arm behind his back, I could feel it popping, I thought, 'Well, this guy's pride just won't let him tap, will it?' So without hesitation, I broke it. I heard it break, and I thought, 'Ah, there, I just broke it.' I was stopped afterward, but even if I hadn't been, continuing to break it more would have been fine by me."
Despite the crowd actually cheering him back, pundits found the act as extremely offensive and unsportsmanlike, among them Dream executive Keiichi Sasahara and Aoki's trainer Yuki Nakai. Yahoo Sports labelled it as on "the top of the all-time list for worst display of sportsmanship in the history of sports". Aoki would later apologize for his behavior in his post fight interview:
"After my fight, I was excited, and so I did something rude that I should apologize for. But that showed just how excited I was over that fight."
As a result of his actions following his win, Aoki was dismissed as an instructor at the Paraestra Kasai gym, though he was still training under Nakai and representing Paraestra.
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.
Nicknamed "Tobikan Judan" ("The Grand Master of Flying Submissions") due to his spectacular submissions, Aoki is considered an unusual fighter for his heavy specialization in grappling at the expense of other areas of the MMA game. Therefore, virtually all of his stand-up game is focused on taking his opponent to the ground, utilizing chain combinations of wrestling and judo techniques from the clinch to secure his goal, as well as the more dramatic guard pulling. Once on the mat, Aoki is an eclectic grappler, drawing strength from his expertise in many different disciplines like Shooto's style of shoot wrestling, judo, jiu-jitsu and Eddie Bravo's 10th Planet Jiu-Jitsu system. He is an active guard player, favouring specially the rubber guard thanks to his flexibility, and is famous for his creative approach to submissions, excelling not only in armlocks and leglocks, but also in neck cranks and more exotic joint locks.