Rouhani sat down with Ayatollah Sistani on Wednesday after visiting the shrine of Imam Ali (PBUH) – the first Imam of Shia Muslims.
Foreign Minister Mohammad Javad Zarif and Ambassador to Baghdad Iraj Masjedi were also present at the meeting.
There have been no reports about the content of their discussions so far. Journalists and photographers are rarely let in to Ayatollah Sistani’s meetings.
Grand Ayatollah Sistani is known as the spiritual leader of Iraqi Shia Muslims and one of the most senior clerics in Shia Islam.
His fatwas have played a significant part in shaping Iraq’s political stage.
In June 2014 – when the Takfiri Daesh terror group unleashed its campaign of destructive in Iraq – Grand Ayatollah Sistani called on his followers to rush to the national army’s help in the fight against the terrorist outfit.
The fatwa helped Shia fighters, Sunni tribesmen as well as Christian and Yezidi volunteers unite under the umbrella of the Popular Mobilization Units (PMU), commonly known as Hashd al-Sha’abi, to reverse Daesh’s gains and ultimately end the terror group’s territorial rule in Iraq in late 2017.
Later on Wednesday, the Iranian president is scheduled to meet with other senior officials and clerics in Najaf.
Rouhani visited the shrines of Imam Hussein (PBUH), the third Shia Imam, and his half-brother Abbas ibn Ali,in the holy city of Karbala on Tuesday.
Heading a high-ranking delegation, Rouhani began his official Iraq visit on Monday, which featured several meetings and the signing of memorandums of understanding for the expansion of bilateral ties in different fields.
In a joint statement, the two neighboring states hailed Rouhani's Iraq visit as a “turning point” in efforts to strengthen “strategic” cooperation based on non-interference in each other’s internal affairs.