Mogherini's spokeswoman Catherine Ray told a press briefing on Thursday that her boss would "raise the topic" of human rights when she visits Tehran for Rouhani's inauguration ceremony on Saturday.
He went on to describe the U.S.as the "most aggressive state in the world", calling on Iran's political leadership to remain steadfast in the face of perceived external threats ranged against it.
Trump has expressed skepticism about the nuclear agreement, which significantly reduced the scope of Iran's nuclear program in exchange for lifting sanctions, and has sought other ways to keep the pressure on Tehran.
The move by Trump is likely to embolden his hardline critics, who say the nuclear deal was a form of capitulation.
He reiterated Iran's stance that the USA legislation signed by Trump amounts to a "hostile" breach of the landmark 2015 nuclear deal.
Earlier on Saturday, the second part of the ceremony was held at the Iranian Parliament -the swearing-in of the president. He has repeatedly criticized the slow pace of economic recovery since most global sanctions on Iran were lifted previous year.
"Iran will never be the first country to start violating" the accord, Rouhani, 68, said in the Iranian parliament, speaking to officials including European Union foreign policy chief Federica Mogherini.
In the meantime, the USA imposed sanctions on Iran have shed shadows over the outcome of the nuclear deal, with President Rouhani vowing to respond to the "US breach of the terms of that deal".
He made the remarks in the inauguration ceremony where the current President Hassan Rouhani was sworn in as president for the second term.
The presidential election in Iran took place on May 19.
It would also apply sanctions to Iran's Revolutionary Guard and enforce an arms embargo.
Chung noted that Iran has enjoyed positive effects, including economic growth, as a result of the historic nuclear deal it signed with six world powers - the United States, Britain, China, Russia, France and Germany.
Recent unilateral sanctions against Iran by the United States were mainly in response to Tehran's growing missile program, the White House said, stressing that Iran's ballistic missile tests were in violation of the resolutions of the UN Security Council.