The four-day event was organised by the Centre for History, Democracy and Reconciliation from Novi Sad and the Association for History, Cooperation and Reconciliation from Golubic.
The conference is important because although the war ended 20 years ago, Serbia-Croatia relations have not been normalised, said Darko Gavrilovic, president of the Novi Sad centre.
"The importance of the meeting is bringing Serbian-Croatian relations to a civilised level," he said. "There is the question if there is any need for this anymore, because of voices from the European Union that there are no more issues between the Serbs and the Croats. But I still see them," he said.
"They exist at football matches, in the street, in the harassment of ordinary people and in everyday life," Gavrilovic said.
Until 1995, Golubic had a population of 500, but only 100 inhabitants remain, mainly elderly Serb returnees.
Three panels will be held at the conference - on refugee returns and the solving of other status and minority issues of Serbs in Croatia and Croats in Serbia through a consistent enforcement of regulations; on extreme nationalism as a source of hatred and prejudice; and on teaching about the Holocaust as a prerequisite for a better future.
A join statement will be adopted at the end of the conference.