Kovač represented Croatia in two World Cups, 2002 and 2006, and has also participated at two European Championships, 2004 and 2008. At World Cup 2006 he played well in defence, however after picking up a second yellow against Japan he missed the final group match against Australia through suspension. Without Kovač, Croatia struggled in defence with his replacement Tomas committing handball for Australia's first goal via penalty kick. Croatia eventually drew 2–2 with Australia but were eliminated from the tournament. With Croatia, Leverkusen, and Bayern, Kovač was teammates with his older brother Niko Kovač. He retired from the national team in the fall of 2009, having captained the team after his brother's retirement in 2008.