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."

The Shanghai Composite benchmark ended 2.2% higher at 4,121.71.
The index crossed the 4,000 mark for the first time since 2008 on Friday.
China's monthly trade data showed its exports fell in March from a year ago by 14.6% in yuan terms, compared with forecasts for a rise of more than 8%.
Imports fell 12.3% in yuan terms compared with forecasts for a fall of more than 11%.
The official numbers mean the country's monthly trade surplus has shrunk to its smallest in 13 months.
Analysts said the export numbers for March were a surprise.
Hong Kong's Hang Seng index closed up 2.7% at 28,016.34 to hit a fresh seven-year high as the market continued to benefit from large inflows of money from mainland Chinese investors through the new stock connect trading link.
Last month, Beijing allowed mutual funds to invest in Hong Kong through the connect plan.
In Japan, the benchmark Nikkei 225 index closed flat, down just 0.01% at 19,905.46 points.
On Friday, the index traded above 20,000 for the first time since April 2000 and it is up nearly 15% this year.
Australian shares were in positive territory early on Monday but lost gains later with the S&P/ASX 200 closing down 0.14% at 5,960.30.
Commodity prices were weighing on shares of some mining companies as iron prices remain depressed.
Australia has said it expects the plunging price of iron ore to slash revenue forecasts by A$25bn (£13bn; $19bn) over the next four years.
Australian Treasurer Joe Hockey told the Australian Financial Review that the price for iron ore, Australia's biggest export, could fall as low as $35 a tonne.
Atlas Iron shares remained suspended. The company said on Friday that it would stop all mining in Australia because iron ore prices were below its breakeven level.
"Despite an extensive cost-cutting programme... the global supply-demand imbalance for iron ore has driven prices down to the point where it is no longer viable for Atlas to continue production," the firm said.
In South Korea, the Kospi share index closed up 0.5% at 2,098.92.
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.
[NEXT_CONCEPT]
Shares in China were higher on Monday as weaker-than-expected trade data from the mainland raised hopes among investors that Beijing may introduce further stimulus measures soon.