Yamamoto began karting in 1994 and won the All-Japan Kart Championship FA class title in 2002. In 2006, he graduated from the Suzuka Circuit Racing School Formula (SRS-F) with a scholarship to compete in Formula Challenge Japan (FCJ). In 2007, he joined the Honda Formula Dream Project (HFDP) academy and finished second in the FCJ championship with two wins. He moved up to the Japanese Formula 3 Championship with Honda Team Real in 2008, finishing fifth in the championship class with one win. In 2009, he moved to the National Class with HFDP Racing (managed by Real Racing) and won the class title with eight wins in sixteen races.
Yamamoto debuted in the Super GT Series in 2010, driving a Honda HSV-010 GT for Team Kunimitsu alongside co-driver Takuya Izawa. He scored a podium on his debut at Suzuka and took another third place at the Suzuka endurance round. During the following two seasons, he scored three more podium finishes and was fifth in the drivers' standings in 2012 — the best result for a Honda driver that season.
In 2013, Yamamoto transferred to the Weider Modulo Dome Racing team and took his first Super GT victory at the Suzuka 1000km endurance race alongside co-driver Frédéric Makowiecki; they finished fourth in the championship. In 2014, he won the summer race at Fuji to take the first win for the new Honda NSX Concept-GT car. Sharing the car across the season with Makowiecki, Izawa, and Jean-Karl Vernay, Yamamoto finished fourth in the championship for the second consecutive season. He returned to Team Kunimitsu in 2015, reuniting with Izawa, won at Sugo, and finished a career-best third in the championship. Over the following two seasons, Yamamoto scored three more podium finishes, including a third place in the 2017 Suzuka 1000km.
Ahead of 2018, 2009 Formula One world champion Jenson Button joined Team Kunimitsu as Yamamoto's co-driver. In their first race together at Okayama, Yamamoto and Button finished second. They finished second again at Suzuka in May, then won at Sportsland Sugo and finished third at Motegi to clinch the GT500 Drivers' and Teams' Championships. It was the first JGTC/Super GT title for Team Kunimitsu, and having won Super Formula earlier that year, Yamamoto became the first driver to win both titles in the same year in fourteen years. Yamamoto and Button finished the 2019 season eighth with two podiums, then Button left Super GT.
Tadasuke Makino joined as Yamamoto's co-driver for 2020. Yamamoto scored seven top-six finishes in eight races, including three podiums. In the final round at Fuji, Yamamoto was running second on the final lap when race leader Ryo Hirakawa of TGR Team KeePer TOM's ran out of fuel coming out of the final corner; Yamamoto overtook Hirakawa to win and clinch his and Team Kunimitsu's second set of GT500 titles in three years.
In 2021, after winning the third race of the year at Motegi with Makino, Yamamoto built a points lead as high as 16 points before the penultimate round. He was in position to win his third GT500 title in four years at the final race at Fuji but was taken out of contention after being hit by GT300 class Honda driver Ren Sato. Yamamoto finished the year third. In the first race for Team Kunimitsu since the death of founder Kunimitsu Takahashi, Yamamoto and Makino finished second at Okayama to start the 2022 season. They ended the year with a win at Motegi from pole position; Yamamoto finished third in the championship for the second consecutive season. After the race, Yamamoto, Makino, and team principal Kazuhiro Kojima carried a portrait of Takahashi to the post-race interviews.
Yamamoto suffered a violent crash during the sixth round of the 2023 season at Sugo, when his car hit the guardrail and flipped over after colliding with a GT300 car along the frontstretch. He was diagnosed with a neck injury that forced him to miss the rest of the Super GT and Super Formula seasons. He recovered in time for the 2024 season, and he and Makino finished third in the opening round at Okayama.
Yamamoto entered the Super Formula Championship (then known as Formula Nippon) in 2010, driving a Honda-powered car for Nakajima Racing. He scored seven top-seven finishes in the eight races of 2010, finished seventh overall, and claimed Rookie of the Year honours. He moved to Team Mugen in 2011 and took pole position at Suzuka in his first race with the team, but did not finish after a first-lap incident.
The 2013 season brought five podiums and a maiden series victory. He finished the year level on points with André Lotterer, who also had more wins. However, the championship tiebreaker in Super Formula at the time went to the driver who scored the most points at the last race meeting at Suzuka; Yamamoto's win and third-place finish in the double-header finale were enough to win the title ahead of Lotterer, who missed the finale due to his FIA World Endurance Championship commitments with Audi.
After the introduction of the new Dallara SF14 in 2014, Yamamoto took five pole positions, four podiums, and two wins (both at Suzuka) from 2014 to 2017, and was the leading Honda driver in the standings in 2014 and 2015. He won his second championship in 2018 with three wins, including the first and last rounds at Suzuka; the latter clinched his title ahead of Nick Cassidy.
Yamamoto switched to Dandelion Racing for 2019, beginning the year with three podiums and a win in the first three races but finishing runner-up behind Cassidy. He won his third championship in 2020, by just two points over Ryo Hirakawa — whom he had also beaten for the GT500 title earlier that year. This made him the first driver to win both the GT500 and Super Formula championships in the same year on multiple occasions, and only the fourth driver to win three or more Japanese Top Formula championships, joining six-time champion Kazuyoshi Hoshino, five-time champion Satoru Nakajima, and four-time champion Satoshi Motoyama.
Yamamoto moved back to Nakajima Racing for 2021 and slumped to a career-worst 13th, failing to win a race or record a podium for the first time since 2014. His winless drought ended at the seventh round at Motegi, where he won a wet race from pole position. His 2023 season ended prematurely after the Super GT crash at Sportsland Sugo; he recorded three top-ten finishes and was 12th in points at the time of the accident.
After winning the GT500 and Super Formula titles in 2018, Yamamoto accumulated the 40 points required for an FIA Super License. In 2019, he drove for Scuderia Toro Rosso-Honda in the first practice session of the Japanese Grand Prix, completing the most laps in the session and setting a fastest lap time just 0.1s off regular driver Daniil Kvyat. This made him the first Japanese driver to drive during a Formula One Grand Prix session since Kamui Kobayashi in 2014. Despite the performance, Yamamoto was not selected by Toro Rosso — which had by then renamed itself Scuderia AlphaTauri — or Red Bull Racing for a race seat in 2020.
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