Ali Akbar Salehi passed through Khartoum and met an official from Sudan's foreign ministry, Sudanese Foreign Minister Ali Karti told reporters, in what he called a "normal protocol" meeting without formal talks.
The date of the visit was not disclosed.
Sudan's links to Iran have come under scrutiny after Khartoum accused Israel of sending four radar-evading aircraft to strike the Yarmouk military factory in the heart of Khartoum at midnight on October 23.
The factory compound exploded and burst into flames, and speculation followed that Iranian weapons were stored or manufactured there.
Sudan's foreign ministry denied Iran had any involvement in the Yarmouk factory, while Israel refused all comment on Khartoum's accusation about the military factory.