The meeting will be attended by police officers, lawyers and Scotland's Lord Advocate James Wolffe QC.
The focus will be on how leaving the EU could affect law enforcement and criminal justice in Scotland.
It will also look at the possible implications for civil and family law, and commercial issues.
The meeting, which will also include experts from the Scottish Universities Legal Network on Europe and the Standing Council on Europe, is due to take place in Edinburgh on 24 November.
Mr Matheson said: "The UK Brexit vote raises many uncertainties for Scotland's unique justice system.
"That is why I am bringing together leaders and experts to help us understand these issues - and any steps we can take now to mitigate the risks.
"The cessation of EU membership and single market access would have significant and wide-ranging ramifications from a justice and legal perspective.
"The issues range from tackling cross-border crime through to an individual with an EU ex-partner securing child maintenance payment, from Europol co-ordination with other countries to protecting Scots consumers' rights when buying from abroad online."
It follows a court ruling that parliament must vote before the UK can start the process of leaving the EU.
The ruling means the UK government cannot trigger Article 50 of the Lisbon Treaty - beginning formal exit negotiations with the EU - on its own.
The justice secretary added: "The summit discussions will help inform us of risks like these - and others - as the Scottish government continues to press for full involvement in all negotiations between the UK government and the EU.
"Despite the uncertainties caused by the threat of Brexit, we will continue our efforts to safeguard Scotland's communities and the integrity of our justice system, while protecting the personal and commercial interests of our families, consumers and businesses."
Justice Secretary Michael Matheson is to host a summit of experts to consider how the UK's Brexit vote could affect Scotland's justice system.