The team debuted at a World Championship event at the Sachsenring circuit in 2001, entering Finnish rider Mika Kallio as a wildcard in the 125cc class. Early machinery carried Honda branding despite using Ajo-supplied engines. Kallio became a full-time competitor in 2002, finishing that season with a Rookie of the Year award ahead of eventual champions Andrea Dovizioso and Jorge Lorenzo. Aki Ajo's son, Niklas Ajo — himself a former 125cc and Moto3 racer — later became team principal as Aki transitioned to manage the factory KTM MotoGP squad.
The team's first major success came in 2003 with a 1-2 finish in Australia, courtesy of Andrea Ballerini and Masao Azuma. After years of steady development and mid-field results through the mid-2000s, Ajo Motorsport broke through to title contention in 2008 when Mike Di Meglio won four races — in France, Catalonia, Germany, and Australia — to clinch the 125cc World Championship, the team's first title.
The 2010 season delivered another title through a dominant campaign by Marc Marquez, who scored twelve pole positions and ten victories to secure the 125cc crown, the team's second in three years.
When the championship transitioned from 125cc to Moto3 for 2012, Ajo adopted KTM machinery. Sandro Cortese won the inaugural Moto3 title that year, with the Red Bull KTM Ajo squad taking five victories and nine podiums across the season. The team continued to develop future stars: Jack Miller narrowly missed the 2014 Moto3 title by just two points, finishing second overall.
Ajo expanded into the Moto2 class in 2015, immediately winning the championship with Johann Zarco, who had rejoined the team after earlier riding for them in 125cc. Zarco defended the Moto2 title in 2016, while simultaneously Brad Binder won the Moto3 championship that same year — a remarkable double title in a single season.
Subsequent Moto2 titles followed with Remy Gardner in 2021 and Augusto Fernandez in 2022. Pedro Acosta provided one of the most spectacular title runs in the championship's history when he won the 2021 Moto3 championship as a rookie, becoming the second-youngest champion in that category's history, with six victories. Acosta then transferred to Moto2 and added a second consecutive world title for himself in 2023, cementing his status as a generational talent developed entirely within the Ajo structure.
Across its history, Ajo Motorsport has launched the world championship careers of numerous riders who went on to compete in MotoGP. Marc Marquez, Brad Binder, Miguel Oliveira, Johann Zarco, Remy Gardner, Augusto Fernandez, and Pedro Acosta all won world titles with the team before graduating to the premier class. Jack Miller, Jorge Martin, and Raul Fernandez are among others who developed under the Ajo program.
The team also participated in the MotoE World Cup from its inaugural 2019 season, with Finnish rider Niki Tuuli winning the opening round before the campaign was cut short by the fire at the Jerez circuit that destroyed all competitor motorcycles.
The team's long partnership with KTM has been central to its identity, with the Austrian manufacturer's Moto3 machinery forming the backbone of its junior class program since 2012. In Moto2, the team initially used KTM chassis before switching to Kalex in 2020 when KTM closed its Moto2 chassis programme. Title sponsorship from Red Bull, which has remained a partner for many years, reflects the team's consistent role as a pathway for riders in the energy drink company's own junior development ladder. For the 2024 season, the team's Moto2 programme shifted to a new lineup as Pedro Acosta graduated to MotoGP, and the team adopted WP suspension in line with its ties to the KTM-Pierer group.
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