Rouhani, who is on a three-day visit to the country, arrived here on Thursday. He visited the tombs along with other Iranian ministers and senior officials accompanying him, amid tight security.
The visiting dignitary went around the complex, housing mausoleums of rulers of the Qutub Shahi Dynasty (1518-1687), who had Iranian lineage.
The officials of the Telangana government briefed Rouhani about the necropolis, which has 72 mausoleums, many of them built in Persian architectural style.
He was also briefed about the restoration project taken up by Aga Khan Trust for Culture.
Rouhani will later visit the historic Makkah Masjid to offer Friday prayers and address the gathering.
The Iranian President on Thursday night addressed Muslim leaders and scholars. He said Iran was keen to strengthen relations with India in all areas of mutual interest.
Hyderabad has historic cultural links with Iran. The city, founded by Quli Qutub Shah, was designed on the lines of Iranian city Isfahan.
Mir Momin Astrabadi, who had migrated from Iran, had prepared the design of Charminar and Hyderabad.