Pogatetz made his international debut for Austria on 18 May 2002 in a 6–2 defeat by Germany. He came on in the 83rd minute as a substitute for Ernst Dospel. His first international goal came on 6 September 2003 in a Euro 2004 qualifying game in the Feyenoord Stadium, Rotterdam. With score at 1–0 to Netherlands, Pogatetz equalised only for the game to finish 3–1 to the Netherlands. On 12 October 2005, he was dismissed in an international game against Northern Ireland. In the 73rd minute in a 2–0 win in the Ernst Happel Stadion in Vienna. Pogatetz retaliated to a "reckless challenge" by Northern Ireland's Damien Johnson. Both were dismissed. In September 2006, Pogatetz was banned from playing for his country after he criticised the coach Josef Hickersberger and captain Andreas Ivanschitz after Austria drew with Costa Rica and lost to Venezuela in an international tournament played earlier in the month. In 2008, he was a member of the Austria team at Euro 2008 which Austria co-hosted with Switzerland. He played all three games, against Croatia, Germany and Poland, as Austria failed to make the knock-out stages of the competition.
