Following the end of the tournament, Fernandes continued to be involved in both friendly and World Cup Qualification matches for the national side. On 28 March 2009, Fernandes scored his first goal for Switzerland, heading in a corner to seal a 2–0 win against Moldova. He then helped Switerzland qualify for the FIFA World Cup after beating Israel on 14 October 2009. In May 2010, Fernandes was called up to the national team squad for the World Cup in South Africa. He scored his first 2010 World Cup goal for Switzerland against eventual winners Spain on 16 June 2010, which Switzerland went on to win 1–0. After this, he was considered as a national hero in Switzerland. However, Switzerland did not advance to the round of 16, after a loss to Chile and a draw to Honduras. Meanwhile, Spain went on to win the World Cup.