During his time with Rijeka, Mijatović also earned himself a place in the Croatian national under-21 team, for which he won a total of 10 international caps between April 1999 and June 2001. He made his debut for the team at the 1999 World Youth Championship in Nigeria, where he played all 90 minutes in every of the four matches played by the Croatian team at the tournament before they were eliminated in the round of 16. He also made four appearances for the team in their qualifying campaign for the 2002 European Under-21 Championship.