Canepa built his early career through Italian domestic competitions, including the Italian Superstock Championship, the Italian Supersport Championship, and the Superstock 600 UEM European Championship. In 2006 he finished runner-up in the European Superstock 600 Championship, which earned him promotion to the full Superstock 1000 class the following season.
In 2007 Canepa won the FIM Superstock 1000 Cup, also referred to as the European Superstock 1000 Championship, riding a Ducati 1098 S. The title opened doors to the highest levels of motorcycle racing and led to a role as a Ducati factory tester for both their MotoGP and World Superbike machines in 2008.
Canepa's versatility as a tester led to broader opportunities. In the second half of the 2008 World Superbike season he received three wild card entries, and at his debut at Brno he qualified on the second row — an impressive result that demonstrated his ability on the Superpole format, in which he had no prior experience.
For 2009 Canepa made the step up to MotoGP full-time with the Pramac Ducati team. Despite high expectations following his Superstock success, the campaign yielded limited results. He subsequently made an uncompetitive start in Moto2 before returning to the Superstock 1000 FIM Cup in 2011, where he finished fifth.
In 2012 Canepa competed in the Superbike World Championship, then returned to the Superstock 1000 class in 2013, where he finished runner-up behind Sylvain Barrier. That near-miss in Superstock 1000 confirmed him among the top riders in production-based racing despite never having broken through to consistent World Superbike success.
The pivotal chapter of Canepa's career came when he transitioned to the FIM Endurance World Championship in 2016, joining the factory GMT94 Yamaha R1 team. He finished the 2016 season in second place overall, an encouraging debut in the discipline.
In 2017 Canepa won the FIM Endurance World Championship outright with Yamaha. The title was historically significant: he became the first Italian rider to win an Endurance World Championship. Endurance racing demands not only raw speed but consistency across 24-hour events and teamwork across multiple riders, and Canepa excelled in this environment.
Alongside his endurance programme, Canepa held a role as a Yamaha Superbike Factory Team test rider, contributing to machine development, and served as a replacement rider for the team when required. He also worked as a coach to World Superbike riders including Alex Lowes and Michael van der Mark during their campaigns.
Canepa remained active in racing into the 2020s. From 2022 he was contracted to RNF Racing in the MotoE World Cup, competing aboard an Energica Ego Corsa in the all-electric single-make series.
He announced his retirement before the 2024 Bol d'Or, but was subsequently called back to race for the factory Yamaha endurance team at the Italian Round of the 2024 Superbike World Championship in Cremona, substituting for Jonathan Rea. His retirement was ultimately confirmed following that appearance, closing a career that had touched virtually every major strand of international road racing.
Canepa's career is notable for its range and adaptability. Starting from Italian domestic championships, he reached MotoGP, achieved historic success in endurance racing, and contributed to Yamaha's technical programme as a long-term factory tester. His 2017 FIM Endurance World Championship remains the defining result of his career and a landmark for Italian motorcycle sport.