Vlaović was a member of the Croatian national football team for over ten years, between July 1992 and August 2002. He won a total of 52 international caps and scored 15 goals for the team (plus a single goal in his only appearance for Croatia B in a friendly against Romania in 2001). As of November 2010, he is tied for the Croatian national team's fourth-best goalscorer of all time, behind Davor Šuker (45), Darijo Srna (19) and Eduardo da Silva (18).
Vlaović made his international debut for Croatia on 5 July 1992 in their friendly match against Australia in Melbourne, during the team's three-match tour through Australia. After the tour, Vlaović only made four international appearances in just over three and a half years, and having undergone surgery to remove a blood clot from his brain in 1995, he was only able to make one appearance in the UEFA Euro 1996 qualifying. However, he started to play regularly for Croatia in early 1996. On 13 March 1996, he scored his first goals for the team in a friendly match against Korea Republic, netting a flawless hat-trick in Croatia's 3-0 victory.
He was subsequently added to the Croatian squad for the UEFA Euro 1996 finals in England, appearing in all of the team's four matches before they were knocked out by eventual champions, Germany, in the quarter-finals. In Croatia's first match at the tournament, against Turkey, he came off the bench to replace Alen Bokšić in the final 20 minutes and scored the only goal of the match in the 86th minute, thus becoming the first goalscorer for Croatia in a major international tournament.
Two years later, Vlaović was a member of the Croatian squad that surprisingly won the bronze medal at the 1998 FIFA World Cup finals in France, their first FIFA World Cup appearance. He appeared in all of Croatia's seven matches at the tournament, although only making one appearance over the entire 90 minutes in the semi-finals against France. In the 80th minute of the quarter-finals against highly favoured Germany, he scored the second goal in Croatia's 3-0 victory, which all but secured the team's place in the semi-finals.
After a year and a half of absence from the national team, Vlaović made his international comeback in January 2001, making an appearance for Croatia B in a friendly match against Romania, also scoring one goal in the match. He went on to make four appearances and score one goal in Croatia's qualifying campaign for the 2002 FIFA World Cup. He was also added to Croatia's 23-man squad for the finals of that tournament, but was left an unused substitute in all three group matches as the team failed to qualify for the knock-out stages. He won his last international cap in a friendly match against Wales on 21 August 2002.