Born in Switzerland, he first made a name for himself with local side Grasshopper Zurich, joining the club as a 16-year-old in 1999 and breaking into the first team shortly afterwards. After winning the Swiss Super League in 2001, he made the move to the Bundesliga the following summer, signing for VfB Stuttgart.
Despite the promise shown by the 193cm-tall Benaglio, he found first team opportunities at a premium in Stuttgart, with Timo Hildebrand the recognised first-choice between the sticks. This lack of action prompted him to move again, this time to Portugal, where he joined for CD Nacional in 2005. After three successful seasons in the Primeira Liga, Benaglio then returned to the Bundesliga, penning a deal with Wolfsburg in 2008.
He has been there ever since, establishing himself as one of the German top flight's most reliable stoppers. That form has also been translated onto the international stage, with Benaglio assuming the role of Swiss No1 on the eve of UEFA Euro 2008 and going on to play all three of his country's group games at the 2010 FIFA World Cup.
After helping VfL Wolfsburg to fifth place in the Bundesliga and a UEFA Europa League berth in 2013/14, Benaglio was one of nine Bundesliga stars named by Ottmar Hitzfeld in the Switzerland squad for the 2014 World Cup in Brazil.