He spent most of his professional career with Stuttgart and Wolfsburg in Germany's top flight, the Bundesliga, winning the 2009 league championship and appearing in almost 300 competitive matches with the latter club.

[9] Benaglio played once for VfL Wolfsburg II in the amateur Regionalliga Nord while recovering from injury on 5 September 2015, in a 6–1 home defeat of TSV Havelse.

[11] He debuted on 13 September in a 1–1 draw away to RB Leipzig in the group phase of the UEFA Champions League,[12] and made his Ligue 1 bow three days later in a 3–0 home win against RC Strasbourg Alsace.

[15][16] A Swiss international since 2006, Benaglio was called up for the 2006 FIFA World Cup as third choice behind Pascal Zuberbühler and Fabio Coltorti, making his debut in a pre-tournament friendly against China on 3 June.

[17] With consistently good club performances the following years, he was promoted to the starting line-up for UEFA Euro 2008 played on home soil, and became the starter subsequently.

On 2 June 2014, he was named in the full side's list for the World Cup finals by national coach Ottmar Hitzfeld,[20] saving a penalty kick from Karim Benzema in the second match but in a 2–5 defeat by France.