The increased exposure Fyssas received playing at the Spiros Louis ensured a rapid elevation to the Greece national side and he made his debut against Finland in 1999.

On 25 January 2004, he was on the bench for a 1–0 away win against Vitória de Guimarães, a game overshadowed by the sudden death of his teammate Miklós Fehér.

After being allowed to leave Benfica in the summer of 2005, Fyssas made the surprise decision to move to Scotland with the Hearts, despite reported interest from England and Germany.

He collected his fourth career winners medal in his first season with the Tynecastle side, when they defeated Gretna in the 2005–06 Scottish Cup final.

He was one of the key players for team that won the Euro 2004 championship in Portugal, a win that shocked the footballing world as Greece were considered 100–1 outsiders before the tournament started.