Born in Rohrbach, Switzerland, Aegerter started his career in motocross. He then competed in the ADAC Pro Junior Cup 125cc class in 2003 and 2004. In 2005 he moved into the equivalent IDM class, where he competed until the end of 2006. Also in 2006, Aegerter was called up by Multimedia Racing to compete in the 125cc World Championship. Aegerter made his world championship debut in the Portuguese Grand Prix replacing fellow Swiss rider Vincent Braillard. He remained with the team for the rest of the season.
For the 2008 Grand Prix motorcycle racing season, he was offered alongside FrenchmanMike Di Meglio by Ajo Motorsport to ride for them. They both accepted it, while Di Meglio has a full factory Derbi RSA 125, he uses only a standard Derbi RS 125 making him the only Derbi rider to use a standard Derbi bike. Results improved however, as he finished 16th overall, peaking with three 8th places – ahead of di Meglio in Spain, and in San Marino and Malaysia.
For 2009, Aegerter stays with the team alongside Sandro Cortese. Both riders use the factory Derbi RSA 125, giving Aegerter hope for a stronger year than 2008. Sixth place in the wet at Le Mans was the highlight of the first half of the season.
Moto2 World Championship
At the 2014 German Grand Prix, Aegerter achieved both his first Grand Prix pole position and victory in his 129th fending off Mika Kallio's advances in the closing stages.[3]
MotoGP test
Kawasaki (2015)
In 2015, Aegerter took part in tests with Akira Kawasaki MotoGP who supplied Kawasaki engines to the Avintia Racing team in MotoGP along with the WSBK riders.[4]
In the 2022 Supersport World Championship, he received a one race ban for unsporting behaviour when leading the championship with nine consecutive wins. After a crash caused by another rider at the first corner of lap one at the Most round, he simulated an injury to try to force a red flag and start the race again.[7][8]