Mogherini was speaking after talks in Ankara on her first trip to Turkey since taking office.
Turkey is under pressure to stem the flow of IS recruits across its borders, which have become a major gateway between Europe and territory controlled by the extremists.
EU capitals are concerned about the possibility of attacks being mounted by the growing number of European nationals returning home after fighting alongside jihadists.
Mogherini said: "We discussed the situation of foreign fighters. It is one of our common interests we have to face -- having good coordination and good strategy to stop the flow on both (sides).
"The work has been going on in the last weeks, with positive developments in information sharing and coordination. I hope that this can create positive results in the coming days and weeks."
Mogherini, travelling with the EU's enlargement and humanitarian aid commissioners, met President Recep Tayyip Erdogan, Prime Minister Ahmet Davutoglu and Foreign Minister Mevlut Cavusoglu.
Mogherini, a former Italian foreign minister who took up the post of EU diplomatic chief on November 1, is to visit refugee camps on Turkey's southern border Tuesday.
On Monday, Mogherini called for a solution to the Syrian crisis "at the root" and sought support from Turkish leaders for the mission of the UN's envoy to Syria Staffan de Mistura, who met in Turkey with Syrian opposition members to discuss his plan to "freeze" fighting in Aleppo.
She said Turkey was key to a solution to the Syrian conflict.
"Turkey knows very well it can play a very relevant role in the region. If we manage to match the role with the EU... I think we could probably advance the solutions, especially the political solution to the crisis in Syria."
'CONCERNS OVER FREEDOMS'
Signup to our newsletter and follow us on Facebook and Twitter!
The high-profile visit comes as the new EU team is seeking to kickstart Turkey's stalled membership negotiations.
"We know that our membership in the EU will present opportunities for both sides," Foreign Minister Cavusoglu told a news conference with Mogherini. "We look to our relations with the EU as win-win."
Turkey, a regional Sunni Muslim power, has barely made progress in membership negotiations with the EU since they formally opened in 2005.
Talks have stalled due to stumbling blocks including a territorial dispute with member Cyprus and opposition from EU heavyweights France and Germany.
Ankara has also drawn the ire of Brussels over its human rights record, while some EU states have reservations about granting membership to such a large Muslim country.
Mogherini raised concerns over the state of free speech, media liberties and the role of women in Turkey which she branded as "real issues" that need to be addressed. "We have to see... steps forward," she said.
EU Enlargement Commissioner Johannes Hahn said one or more chapters could open in Turkish-EU accession talks in the future.
"We welcome recent moves and signals from member states, and therefore... I am hopeful that it might be possible to open one or the other chapter in the next presidency," he said.
"Things are moving in the right direction."
The EU delegation visited just a week after Russian President Vladimir Putin was in Turkey to announce the cancellation of the multi-billion-dollar South Stream pipeline project.
Putin blamed the EU for throwing obstacles in the path of the project and said Russia would work with Ankara on a new gas hub instead.
Mogherini ruled out any competition between Russia and Brussels over Turkey and said the EU group's visit was not an attempt to "balance" Putin's trip, stressing that the EU was still Turkey's number one trade partner.
"We explicitly welcome if Turkey could become an energy hub for the region," Hahn said.
Turkey has so far resisted pressure from Brussels to join sanctions imposed on Russia for its role in the Ukraine crisis.