A regular in the Croatia national football team, he had earned 45 caps and scored five goals as of the end of 2004. Rapaić played two games for his country at the 2002 FIFA World Cup. He will be most remembered for his spectacular goal scored against Italy. He also played three games for Croatia in Euro 2004 and scored one goal.
He has proved a fan favourite with his fun-loving playing style wherever he has played, and after impressive performances he once again earned a call up in August 2006 for the Croatian national side after missing the 2006 FIFA World Cup. Croatia went on to beat the world champions Italy 2-0 in Livorno, with Rapaić playing a large role.