The Serbian National Council was founded by virtue of the Erdut Agreement and The letter of the Government of the Republic of Croatia on the completion of the peaceful reintegration of the areas under the transitory government which guarantee local minority self government to Serbs. The SNC was founded on the basis of the centuries long tradition of Serbian self government, which goes back to the times of first church/public assemblies, via legal and political acts regulating the position of Serbs in Croatia during the 18th and 19th centuries, to the documents of the State Antifascist Council. The founding assembly meeting of the Council was held in 1997 in Zagreb at the incentive of the Alliance of Serbian Organizations and its members: Serb Cultural Association Prosvjeta, Serbian Democratic Forum, Community of Serbs from Rijeka and Istria as well as the Joint Council of Municipalities (ZVO). Apart from the founding initiators, founding members were also Independent Democratic Serb Party (SDSS), Baranja Democratic Forum, Association of Serbian Refugees and Expellees from Croatia, representatives of some church parishes of the Serbian Orthodox Church, Members of Parliament of Serbian ethnicity and respectable individuals.

Following the adoption of the Constitutional Act on the Rights of National Minorities in 2002, the organizational structure of ethnic minorities’ councils was changed as well. Members of councils are elected by secret ballot, in elections organized by State (so far, four rounds have been held - in 2003, 2007, 2011 and 2015) in all local self government units, where the Serb population exceeds the threshold of 1,5 percent. At the municipality level, the council is elected if there are at least 200 members of the Serb community living there. At the county level this number amounts to 500. In a case when there are at least 100 members, a council's representative is elected.

The SNC network consists of 94 councils with the total of 1581 councilors.