Tsuboi began single-seater racing in 2012 in Formula Challenge Japan, finishing seventh in his debut season and fifth the following year with two victories. After that series closed, he entered the 2014 JAF Formula 4 regional championship and finished second in the FC class, the same year he officially joined the Toyota Young Driver Program. In 2015 he moved to the inaugural FIA F4 Japanese Championship with TOM'S Spirit, won seven races, and claimed the title by just three points over Tadasuke Makino.
Tsuboi contested three seasons of Japanese Formula Three with TOM'S from 2016 to 2018. After finishing third in 2016 without a race win and second in 2017, he dominated the 2018 season with a Japanese F3 record 17 victories in 19 races. The championship was not without incident: at the 2018 Macau Grand Prix FIA Formula 3 World Cup, Tsuboi and German driver Sophia Flörsch were involved in a serious accident when Flörsch's car became airborne after contact with Jehan Daruvala. Both drivers were hospitalized, though Tsuboi escaped without serious lasting injury.
Tsuboi entered Super GT in 2017 in the GT300 class for JMS P.mu LM Corsa, finishing third in the standings that year with a race win at the Fuji 500 km and another at Chang International Circuit. A one-off GT500 outing for Lexus Team SARD at the 2018 Fuji 500 km yielded a second-place finish in his first GT500 race.
His full-time GT500 career began in 2019 with Lexus Team WedsSport Bandoh alongside Yuji Kunimoto. He moved to the new ROOKIE Racing team in 2020 and stepped up to TGR Team au TOM'S in 2021 alongside Yuhi Sekiguchi. Heading into the 2021 season finale at Fuji trailing leader Naoki Yamamoto by 16 points, Tsuboi won the race for his first GT500 class victory. Yamamoto was eliminated in a collision with a GT300 car with 15 laps remaining, handing Tsuboi and Sekiguchi the championship — the largest final-round deficit overcome in Super GT GT500 history.
Tsuboi won his second GT500 title in 2023 alongside Ritomo Miyata, who joined him at TOM'S after Giuliano Alesi's single season with the team in 2022. The pair won four races including back-to-back victories at Autopolis and Motegi, clinching the title by a 29-point margin. In 2024, paired with Kenta Yamashita, Tsuboi became the first driver in GT500 history to win three consecutive championship races, opening the season with a victory at Okayama. He claimed his third GT500 title that year alongside his Super Formula crown. His fourth GT500 championship followed in 2025, tying Quintarelli's all-time record, and he finished as Super Formula runner-up that season.
Tsuboi stepped up to Super Formula in 2019 with JMS P.mu/Cerumo-INGING, recording a second-place finish in a wet race at Fuji in his debut season. He improved to third in the championship in 2020, winning twice. After a difficult 2021 season and several more years with Cerumo-INGING, he joined Vantelin Team TOM'S in 2024. He won his first Super Formula championship that year with three race victories and seven podiums, beating Tadasuke Makino and Tomoki Nojiri. He retained his TOM'S seat as defending champion in 2025 and finished runner-up.
In August 2025, Tsuboi drove a Formula One car for the first time at Fuji Speedway with the Haas F1 Team as part of the Testing of Previous Cars programme.
Tsuboi's four Super GT GT500 championships place him among the most decorated Japanese racing drivers of his generation. His combination of Formula Three dominance, multiple GT500 titles, and a Super Formula championship makes him one of the most complete Japanese drivers produced by the Toyota Young Driver Program.