Fernandes was eligible to play for Switzerland and Cape Verde. His progress attracted interests from the Switerzland Youth Team, playing from the U16 to U21 sides. On 26 April 2006, he made his Switzerland U21 debut, in a 3–3 draw against Romania U21. Fernandes was captain of the Switzerland U-21 that played against the England U21 side in their Euro 2007 qualifying match, becoming the first player with African roots to do so. He went on to make nine appearances for the U21 side.