Union Minister of State for Power R K Singh and Telangana and Andhra Pradesh Governor ESL Narasimhan received him at the Begumpet airport.
"He is scheduled to address Muslim intellectuals, scholars and clerics in the city at 6.30 pm today," an official said.
During his two-day visit to the city, President Rouhani, who is accompanied by a 21-member delegation, will also meet people of Iranian-origin living in Hyderabad.
He will address a congregation at the historic Mecca Masjid in Hyderabad tomorrow after offering Friday prayers, the official said, adding that religious scholars will also participate in the session.
This is Mr Rouhani's second visit to Hyderabad and the first after becoming president.
He would stay at the Taj Krishna hotel tonight, and leave for New Delhi tomorrow evening.