Aegerter began racing in motocross before moving into the ADAC Pro Junior Cup 125cc class in 2003 and 2004. He stepped up into the German IDM 125cc class from 2005 to 2006, and his performances there earned him a call-up by Multimedia Racing to compete in the 125cc World Championship. He made his world championship debut at the Portuguese Grand Prix in 2006, substituting for Swiss compatriot Vincent Braillard.
Aegerter continued his 125cc career from 2007 through to 2009, racing for Ajo Motorsport in 2008 and 2009 aboard Derbi machinery alongside teammates including Mike Di Meglio and Sandro Cortese. Progress was gradual, with best finishes of 8th at several rounds in 2008.
He spent several seasons in the Moto2 World Championship, a period that produced the standout result of his Grand Prix career. At the 2014 German Grand Prix at the Sachsenring, Aegerter claimed both pole position and race victory in his 129th Grand Prix start, holding off Mika Kallio's challenge in the closing stages. It was his first and only Grand Prix victory.
Aegerter participated in testing with Kawasaki in 2015 through the Avintia Racing connection, and in September 2022 rode a Suzuki GSX-RR at a mid-season test at the Misano World Circuit Marco Simoncelli as a stand-in for an injured regular Team Suzuki Ecstar rider.
Aegerter's move to the World Supersport Championship transformed his career. In 2021, competing with Ten Kate Racing Yamaha, he won the Supersport World Championship title — his first world title after years in the Grand Prix system.
He successfully defended the championship in 2022, though the season included controversy: Aegerter received a one-race ban for unsporting behaviour after simulating an injury at the Most round following a crash caused by another rider, in an attempt to force a red flag restart while he was leading the series with nine consecutive wins. Despite the suspension, he secured the title for a second consecutive year.
Also in 2022, Aegerter added the MotoE World Cup to his list of achievements, making him a double world title holder in a single season across two distinct categories.
Having secured back-to-back Supersport world titles, Aegerter moved up to the Superbike World Championship in 2023 with the GRT Yamaha WorldSBK Team, becoming the first Swiss rider to reach a World Superbike podium. He continued to develop his Superbike programme, also using wildcard appearances in the Italian CIV Superbike Championship as additional preparation.
Aegerter has participated in the Suzuka 8 Hours endurance race for Suzuki, reaching the podium twice in the event, adding an endurance dimension to a career primarily built in sprint racing formats.
Aegerter's dual 2022 world titles — Supersport and MotoE — represented an exceptional season in a career that had spent years searching for consistent results at the top level. His transition from long-serving Grand Prix journeyman to double world champion underscores the value of persistence and the opportunity that comes with finding the right machinery and championship environment.