Benaglio captained the Swiss team at the 2012 Olympics, and played nine times during the 2014 World Cup qualification campaign, keeping six clean sheets. On 2 June 2014, he was named in the full side's list for the World Cup finals by national coach Ottmar Hitzfeld, saving a penalty kick from Karim Benzema in the second match but in a 2–5 defeat by France.
