After the 1998 World Cup, Šuker featured for Croatia in their unfruitful run to qualify for the Euro 2000. Šuker was though noted in endeavouring to keep Croatia's hopes alive when he scored a 94th-minute winner against the Republic of Ireland at Maksimir Stadium in Zagreb. The win ensured Croatia would have a strong chance of still qualifying for the tournament. The Croatians would miss out on such in their final qualifier, a 2–2 draw at home to Yugoslavia. Šuker did score a late disallowed goal which, if stood, would have assured Croatia's qualification. He finished with four goals in seven matches during the campaign.