The fire was put out by local firefighters, and the damage is some 60,000 kuna. Nobody was injured.
The van had transported members of Belgrade's 'Partizan' swimming club to Zagreb where they were taking part in an international sporting event.
A police investigation established that an unknown perpetrator set the van on fire.
The police have not reported whether the incident might be connected with another earlier incident in Zagreb when three Serbian students took pictures of themselves bearing the image of Chetnik leader Draza Mihailovic at Zagreb's central square. The students, one male and two female, were arrested after citizens reported what they were doing. The students came to Zagreb as part of a group of some 30 students to see the "Dora Maar and Picasso" exhibition. Their questioning at the magistrate's court in Zagreb is under way.