Emerton played in both legs of World Cup play-off against Uruguay in November 2005, when the Socceroos qualified for the 2006 FIFA World Cup in Germany, the first time that Australia had reached the finals of the World Cup since 1974, and was named in the Australian squad for the World Cup finals. He was in the starting line-up for all three Group Stage games against Japan, Brazil and Croatia as Australia qualified for the second round. However, he received two yellow cards against Croatia, was sent off in the 87th minute and subsequently missed the Socceroos' second round match against Italy.