Yamamoto began practicing Kyokushin karate as a schoolboy and won the all-Japan junior high school full contact karate championships in 2000, followed by the high school championships the following year. He would later begin kickboxing under the legendary Toshio Fujiwara at the Fujiwara Gym in Tokyo, and debuted professionally with a unanimous decision win over Hideki Shimizu at AJKF: Golden Trigger on September 6, 2002.
After amassing an undefeated record of 7-0-2 fighting in the All Japan Kickboxing Federation, Yamamoto was invited to compete in the promotion's Strongest Lightweight Tournament 2004. Having defeated Hiromasa Masuda by unanimous decision at the tournament's opening round on March 13, 2004, he then tasted defeat for the first time at the hands of the eventual tournament winner, Tsogto Amara, when he lost a majority decision in the quarter-finals on April 16, 2004.
He rebounded with three straight victories to earn himself a shot at the AJKF Featherweight (-57 kg/126 lb) Championship against Genki Yamamoto at the Fujiwara Festival 2004 on December 5, 2004. After five rounds of fighting, the bout was called a draw, meaning Genki kept the title.
2005 saw Yamamoto wear gold for the first time in his career by winning the IKUSA 2005 –60 kg/132 lb Grand Prix. A first round knockout of Koishiwara at the quarter-final stage on June 18, 2005 was followed up by a points victory over Tomohiro Oikawa in the semis and then a technical knockout win against Naoki Ishikawa in the final on the same night three months later as Yamamoto claimed the crown. This led him to a rematch with Genki Yamamoto for the AJKF Featherweight title on January 4, 2006 at the New Year Kick Festival 2006, where he won a majority decision and became the new Japanese champion.
Yamamoto then went through a rough patch, however, as he went 2-3-1 in his next six fights with all three losses against Thai opposition. At the end of 2007, he was given the chance to get back on track by entering the AJKF's Best of 60 kg Tournament 2007. A second-round knockout of Susumu Daiguji on August 25, 2007 sent him into the semi-finals two months later where he took a unanimous points victory over Naoki Ishikawa, in what was the third fight between the pair. Later that night, Yamamoto defeated Seimei Otsuki by the same margin in a five-round affair to emerge as Japan's top kickboxer at 60 kg/132 lb.
On January 4, 2008, he made the first and only defence of his AJKF Featherweight strap by knocking Yosuke Mizuochi out with a high kick in round four at the New Year Kick Festival 2008. After being stopped by Muay Thai exponents PKP Rachanon F16 and Wanrop Weerasakreck in his next two outings, he then returned to winning ways with four consecutive victories which earned him a call up to fight on kickboxing's biggest stage, K-1. Making his promotional debut at the K-1 World MAX 2009 World Championship Tournament Final 16 in Fukuoka, Japan on April 21, 2009, Yamamoto outpointed Yuki to a unanimous judges' decision after flooring his opponent with a knee strike in the third and final round.
Despite a knockout loss to Yuji Takeuchi in his next fight at Krush.3 less than a month later, he was asked to fight in the Krush Lightweight Grand Prix 2009. The tournament kicked off with the first round and quarter-finals on July 24, 2009 and Yamamoto defeated both Junpei Aotsu and Seimei Otsuki by decision to advance to the final stage on November 2. He met Genki Yamamoto for the third time in the semis and an extension round was needed to separate them, after which Masahiro was given the nod to advance to the final where he went up against Yuta Kubo. Yamamoto sent Kubo to the canvas late in the third round of a back-and-forth war to secure the unanimous decision victory and the third tournament title of his career.
Having already established himself as arguably the top kickboxer at 63 kg/138 lb, Yamamoto returned to K-1 as one of the favourites to win the K-1 World MAX 2010 –63 kg Japan Tournament. He was drawn against Tetsuya Yamato in the opening stage of the tournament held at the K-1 World MAX 2010 -63kg Japan Tournament Final 16 in Tokyo on May 2, 2010 and suffered a significant upset when he was beaten via unanimous decision after an extension round by the unfancied Yamato who would go on to win the whole tournament.
Even after two losses in a row following a points defeat to Ryuichi Mukaiyama under Muay Thai rules, Yamamoto was still being held in high regard and was recruited by the European It's Showtime promotion to challenge for Sergio Wielzen's It's Showtime 61MAX (-61kg/134lb) Championship. In his international debut and first attempt at a world title, he met Wielzen at Yiannis Evgenikos presents: It’s Showtime Athens on December 11, 2010 in Athens, Greece. Yamamoto was floored by a knee to the body in round one and was stopped from continuing on the doctor's orders in round three due to cut above his right eye, losing by TKO.
Yamamoto then returned to Japan and racked up a record of 4-0-1 throughout 2011 and early 2012 to earn himself another shot at the It's Showtime 61MAX belt, which was now around the waist of Javier Hernandez. The run included decision wins over Arito Tsukahara, Kan Itabashi and Genki Kanazawa under the It's Showtime Japan banner. Hernandez and Yamamoto faced off at Street Culture, Federación Canaria de Kickboxing & Fightclub Group present: It's Showtime 59 in Tenerife, Spain on July 21, 2012, and Yamamoto become the new world champion by unanimous decision after using good boxing and knees to outpoint the Spaniard.
He was expected to fight on an It's Showtime card in Yokohama, Japan on November 17, 2012 but the event was cancelled following the promotion's acquisition by Glory.
He was ranked at #2 behind Masaaki Noiri when the lightweight world rankings were first published by LiverKick in September 2012, but he slipped down to #3 come November as Karim Bennoui nipped in front of him.
On December 2, 2012. Yamamoto faced Dutch import Mansour Yaqubi at RISE/M-1 ~Infinity~ in Tokyo, Japan. Despite being floored by Yaqubi at the beginning of the third round, he was able score three knockdowns for himself before the final bell, forcing a referee stoppage.
He defeated his third international opponent on the bounce when he took an extension round unanimous decision over Karim Bennoui at RISE 92 on March 17, 2013 in Tokyo.
Yamamoto got his revenge over Sergio Wielzen at RISE 94 in Tokyo on July 20, 2013, knocking the Surinamese fighter out with a second round high kick. With this win, he defeated the three other It's Showtime 61MAX Champions.
He participated in La 20ème Nuit des Champions -62 kg/136 lb tournament featuring four of the world's best lightweights in Marseille, France on November 23, 2013, losing to Yetkin Özkul on points in the semi-finals to exit the competition.All Japan Kickboxing Federation
AJKF Featherweight (-57 kg/126 lb) Championship
AJKF The Best of 60 kg/132 lb Tournament 2007 Champion
IKUSA 2005 –60 kg/132 lb Grand Prix Champion
It's Showtime 61MAX (-61kg/134lb) Championship
Krush Lightweight (-63 kg/138 lb) Grand Prix 2009 Champion