Although selected for Yugoslavia squad at the 1990 FIFA World Cup in Italy, the 20-year-old Bokšić did not play in the tournament, with coach Ivica Osim preferring more experienced forwards in the lineup. Following Croatia's independence from Yugoslavia Bokšić became an integral part of Croatia's national team in the 1990s under coach Miroslav Blažević. He played for Croatia at the 1996 European Championship but was not included in the squad for the 1998 FIFA World Cup in France due to an injury he suffered only weeks before the tournament. Bokšić finally made his World Cup debut at the age of 32 at the 2002 FIFA World Cup in Japan, appearing in all three of the team's group stage matches, before retiring only a year later in 2003.