Ms Mogherini and other top EU officials will urge Turkey to stop the flow of foreign fighters across its borders.
She will emphasise the "strategic importance" of their relationship, a week after Russian President Vladimir Putin made a similar visit.
Ms Mogherini will also urge Turkey to support EU sanctions against Russia.
In an interview with the BBC's Lyse Doucet, Ms Mogherini said that while the crisis in Syria was not something that could be solved from Brussels, the EU still had a role to play, including "the empowerment of more actors that might take the lead".
"I am sure that the UN can play some sort of a positive role," she said.
The EU wants Turkey to help identify foreign fighters and provide warnings of any danger to aviation security, an unnamed EU official told the Reuters news agency.
EU officials want Turkey to provide more help and support in the fight against IS - and other Middle Eastern militant groups - as part of an initiative to restrict their funding and curtail the flow of foreign fighters.
"The visit... is a strong indication of the strategic importance of the EU-Turkey relationship and our desire to step up engagement," Ms Mogherini said in a statement.
Negotiations over Turkish membership of the EU have been going on since 2005, but have been held up because of disagreements over the divided island of Cyprus and resistance to Turkish EU membership from some member countries.
Russia policy
Our correspondent says that recently-appointed Ms Mogherini is gradually developing her approach to the large number of issues now confronting the EU including the continuing crisis in Ukraine.
The visit of the EU delegation follows that of Russia's President Vladimir Putin last week, during which he announced that Russia was abandoning plans a gas pipeline under the Black Sea and through Bulgaria to central and southern Europe, known as the South Stream project.
Instead of South Stream, Mr Putin said Russia hoped to establish an alternative route via Turkey, setting up a hub on its border with Greece,
Russia and Turkey are major trading partners. Russia provides the bulk of Turkey's gas requirements and is set to build Turkey's first nuclear power plant.
Turkey has not imposed sanctions on Russia over its annexation of Crimea, and the EU is urging it to do so, or at least not to increase trade with Russia to fill gaps left by suspended EU exports.
Refugee appeal
Thousands of Europeans have travelled to fight in Syria with Islamic State or other militant groups, and for them Turkey is a key transit point.
Turkey argues that EU governments should be working harder to prevent putative fighters from travelling to the region. It argues that it has had to make big sacrifices in accommodating thousands of Syrian refugees.
More than 30 humanitarian organisations have launched an appeal for countries to take in 180,000 refugees from the Syrian conflict, representing about 5% of the projected refugee population by the end of 2015, according to the Office of the UN High Commissioner for Refugees (UNHCR).
The issue will be discussed at a conference in Geneva on Tuesday.
(BBC)
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