In 2003 Stoner moved to the 125cc GP category.
Here, working again with Cecchinello and Aprilia,
he met with considerable success, scoring his
first GP race win and three second places, finishing
8th overall at the season's end.
In 2004 Stoner joined the Red Bull KTM factory
team in 125cc class and continued to improve,
with another race win, two second places, three
thirds, and a final championship position of fifth.
In 2005 he rejoined the 250cc world championship
class, racing once again for Lucio Cecchinello
on an Aprilia. Onboard a factory Aprilia, Stoner
emerged toward the season's end as a serious threat
to championship leader Dani Pedrosa; a threat
that only dissipated with a crash at Stoner's
home Grand Prix of Phillip Island, allowing Pedrosa
to establish an insurmountable points lead. Stoner
went on to claim a solid second place in the overall
championship standings, with an impressive five
race victories for the season.
Stoner was in advanced negotiations with Yamaha,
but after they dropped them he settled on an alliance
once more with team manager Lucio Cecchinello
on a Honda RC211V, on a one-bike team new to the
series for the 2006 Season. He took pole for only
his second race, but crashed several times. He
finished his debut season in 8th position with
his best result being a 2nd place at the Turkish
GP, where he was overtaken on the final corner
by Marco Melandri.
Stoner secured a ride with the factory Ducati
team for the 2007 season, joining Loris Capirossi
on the new 800cc Ducati Desmosedici GP7. He recently
signed a contract extension with Ducati that will
see him remain with the team for the 2008 and
2009 seasons (in which he will partner Italian
Marco Melandri), with a further option for a 4th
season in 2010.