Fernández made his Grand Prix debut in Moto2 at the 2017 Italian Grand Prix as a replacement for Axel Bassani at Speed Up Racing, remaining with the team through to the end of the season and scoring six points in total.
Fernández began 2018 in the Moto2 European Championship before being called up to the Grand Prix paddock to replace Héctor Barberá at Pons Racing after Barberá was dismissed from the team. He impressed immediately, scoring points in his first four races, and closed the year with sixth at Motegi, fourth in Australia, and eighth in Valencia. He finished eighteenth in the standings with 45 points — 35 more than Barberá had managed.
His 2019 season started with a fifth place in Qatar before a double wrist fracture in a heavy practice crash in Argentina cost him two races. Returning at Jerez, he immediately stood on the podium, and backed it up with another third place at Le Mans the following weekend. He then secured his first pole position in the class at Barcelona and, two weeks later at Assen, took his maiden Moto2 victory after championship contenders Álex Márquez and Lorenzo Baldassarri crashed out of the lead together. Fernández added wins in Britain and at Misano, ending the season fifth in the standings with 207 points.
Fernández joined Marc VDS Racing for 2020 alongside Sam Lowes, stepping into the seat vacated by the promoted Álex Márquez. The season was difficult; his best result was a fourth place in France and he finished thirteenth in the standings with 71 points.
In 2021 the season began poorly with four retirements in the first eight races, but Fernández recovered strongly. He collected six podiums across the last ten rounds — including a second place at Rimini — and returned to fifth in the final standings with 174 points.
Red Bull KTM Ajo signed Fernández for 2022. He won four races across the season and edged out Honda's Ai Ogura in a close title fight to become the 2022 Moto2 World Champion.
Fernández graduated to MotoGP in 2023 with GasGas Factory Racing Tech3, partnering Pol Espargaró. His best result was a fourth place at the French Grand Prix after qualifying twelfth, and he scored enough points to demonstrate competence at the premier level. For 2024 he was partnered with hotly-tipped rookie Pedro Acosta under the same team banner. Fernández managed 27 points across the season and finished twentieth in the championship.
After KTM chose not to retain him for 2025, Fernández announced he would become a Yamaha factory test rider before Yamaha made any official statement — a noteworthy breach of protocol that underlined the informal state of his deal at the time. Yamaha officially confirmed the role in December 2024, with provision for up to six wild-card race entries.
Fernández made his Yamaha race appearances as a wild-card and injury replacement. In 2025 he substituted for the injured Miguel Oliveira at Prima Pramac Yamaha at the Americas, Qatar, and Spanish Grands Prix, taking a thirteenth place in the USA. He signed an extension to remain as Yamaha's official test rider through the 2026 and 2027 seasons in September 2025.
Fernández's Moto2 championship in 2022 was earned against stiff opposition and placed him among the stronger graduates of recent intermediate classes. His transition to a test role reflects Yamaha's need for experienced development feedback at a time when the manufacturer was working to restore competitiveness in MotoGP after a difficult period for the Japanese factory.
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