Saudi officials greeted Foreign Minister Mohammad Javad Zarif after he landed at a military airport in the capital Riyadh.
Iran and Saudi Arabia, the region's foremost Shiite and Sunni Muslim powers, have had troubled relations in recent years after taking different sides in the Syrian civil war.
Tehran has backed Syrian President Bashar al-Assad while Riyadh supported Sunni rebels trying to topple him.
Zarif has previously declined a Saudi invitation to visit the kingdom, citing continued negotiations between his country and international powers over Iran's disputed nuclear programme.
That was the first high-level Iranian visit to the kingdom since Hassan Rouhani became the Islamic republic's president a year earlier.
They discussed the fight against Islamic State group jihadists, who both nations oppose.
Rouhani has stated his wish to improve relations with Iran's neighbours, especially Saudi Arabia.
Since the June 2013 election of Rouhani, regarded as a moderate, Iran has engaged in a diplomatic push with Riyadh but relations have soured in recent months over the falling global price of oil.
Iran has been among the oil exporting countries worst hit by the price fall.
Rouhani expressed his condolences after the death yesterday of Saudi King Abdullah, who has been succeeded by his half-brother Salman.
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