Deputy Foreign Minister Hossein Amir-Abdollahian flew to the desert kingdom on Monday to meet Foreign Minister Prince Saud al-Faisal and discuss "matters of common interest", the reports said.
No further information was immediately available about the trip, the first by a high-level official from Shiite Iran to Sunni-ruled Saudi Arabia since Hassan Rouhani became the Islamic republic's president in August last year.
"It is a step towards improving relations between Tehran and Riyadh," Iran's financial daily Donya-e Eghtessad wrote.
The authorities in Saudi Arabia had invited Iranian Foreign Minister Mohammad Javad Zarif, but he declined, citing the ongoing nuclear negotiations between Iran and the P5+1 powers.
Donya-e Eghtessad also quoted Amir-Abdollahian as saying a Zarif trip to Riyadh should "be prepared and protocol must be respected".
Rouhani has stated his wish to improve relations with Iran's neighbours, especially Saudi Arabia, the Gulf's other regional heavyweight.
The two countries are on opposite sides in the Syrian conflict, with Tehran backing President Bashar al-Assad and Riyadh supporting the rebels trying to topple him.
"I advise Muslim countries that support the terrorists with their petrodollars to stop," Rouhani said, referring to Saudi Arabia and Qatar which Tehran accuses of financing the jihadists.
"Tomorrow you will be targeted... By these savage terrorists. Wash your hands of killing and the killing of Muslims," he added.
Tehran also supports protests by Bahrain's Shiite majority while Riyadh backs its Sunni rulers.
Saudi Arabia is also concerned about Iran's nuclear programme and fears a rapprochement between Tehran and the United States in the context of an agreement on the nuclear issue.