The patient had been hospitalized for several days, according to the center.
Iranian health ministry has advised those in contact with the livestock to take precautions against the viral disease.
Endemic in Africa, Asia, the Middle East and the Balkans, the disease causes severe bleeding.
People usually catch it through contact with the blood of infected animals.
Symptoms of the disease may include fever, muscle pains, headache, vomiting, diarrhea, and bleeding into the skin. Complications may include liver failure.
Iran’s neighboring country, Iraq, is experiencing a sharp uptick in the number of Congo fever cases which is feared to spread the disease.
Iranian officials say the surge in Iraq can cause the spread of the disease as there are no vaccines to curb it yet.