Mogherini, who was the lead negotiator for the six powers who struck the deal, was accompanied by other top EU officials. She was to meet Iranian Foreign Minister Mohammad Javad Zarif.
Her one-day trip comes after Iran raised concerns about banking sanctions, with officials saying the West, particularly the United States, is still creating hurdles to its access to the global financial system.
Yesterday, the governor of Iran's Central Bank said the international community was not sticking to its promises.
The six powers led by the United States agreed in July last year to lift sanctions that had locked down much of the Iran's economy for years in exchange for limits on Tehran's nuclear programme.
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The move allowed Iran to resume a higher level of oil exports when the deal was implemented in January, as well as opening up more trade opportunities.
But with the US still maintaining some sanctions on the country, Iran's access to global finance remains limited.
"They have been asked not to work with Iranian banks, and they're afraid," he said.
"It's because of the heavy penalties that have been imposed upon them," he said, referring to huge fines imposed in the past.
Ahead of her trip to Tehran, Mogherini said banking, investment and trade were on the agenda of her talks, as well as the conflicts in Syria and Yemen, where the West has been looking for Iran's cooperation with peace efforts.