His international career began in 2015, when he competed in the FIM CEV Repsol Moto2 International Championship. In 2016, and at the minimum age permitted for the category, he made his debut in the Moto2 World Championship with the CarXpert Interwetten team, riding a Kalex bike over six rounds as a replacement for Dominique Aegerter.

Lecuona remained with the same team for the following three seasons, still on the Kalex in 2017 and then, in 2018 and 2019, on a KTM with which he achieved two podiums, at Valencia in 2018 (second) and in Thailand in 2019 (third). He made his MotoGP debut at the last round of the season in Valencia.

He became a full-time Tech 3 rider in the MotoGP World Championship in 2020. Despite entering the class during the most difficult period of the Covid-19 pandemic, the rookie ran a solid season, scoring three top-ten finishes. Showing a determination and speed that have often seen him fight on equal terms against some much more experienced opponents, Lecuona finished his second MotoGP season in 20th position overall, with three more top-ten finishes including a strong sixth-place finish at the Austrian GP as his best result.

Signed by Honda to be a factory HRC rider in 2022, Lecuona enjoyed an impressive rookie season and achieved his first podium already at round 2 (placing third at Assen). Battling in the top five during most of the subsequent races, the Catalunya round saw Lecuona put Honda and the Fireblade back on pole position for the first time since 2016 (Michael van der Mark, Buriram). Unable to compete in the final two rounds due to injury, the young Spanish rider placed ninth overall at the end of the season. Adding to what was already a strong year, Iker teamed up with BSB rider Takumi Takahashi and HRC official test rider Tetsuta Nagashima to compete in the Suzuka 8 Hours on 7 August 2022 August. The team scored an historic debut victory, which marked the 28^th win for Honda in the famous endurance race, and its first since 2014. The riders competed with factory bikes based on the CBR1000RR-R FIREBLADE SP and also set pole position with an all-time record lap of 2:04.934 and the fastest lap of the race, completed in 2:06.930 (both by Nagashima).

The young Spaniard remained with the team for the 2023 WorldSBK championship, where he again battled in the top five on many occasions. Iker represented HRC in the MotoGP Championship as much as 7 times in 2023, as a replacement-rider for the Repsol Honda Team and LCR Team.

Having been the standard-bearers for Honda in the Superbike World Championship in 2022 and 2023, with both making an impression on and off the track for their talent, speed, and positive attitude, Honda Racing Corporation announced  a contract extension with both Iker Lecuona and his teammate Xavi Vierge for the next two years (2024-2025).