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.

Aegerter continued with Multimedia Racing for the 2007 Grand Prix motorcycle racing season and still had Italian teammates Raffaele De Rosa and Simone Grotzkyj. He had a very slow start only managing to score back to back 15th place at the 2007 Catalan motorcycle Grand Prix and at the 2007 Dutch TT, and later at the wet 2007 Japanese motorcycle Grand Prix at 11th place. This championship points scoring finishes only manage he finished at 23rd place with 7 points.

For the 2008 Grand Prix motorcycle racing season, he was offered alongside Frenchman Mike 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

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