The border post at Khosravi, around 570 kilometres (350 miles) east of Tehran, was shut during the night and was still closed as of Thursday afternoon.
It comes as Iranians head to the Iraqi holy city of Karbala for an annual Shiite pilgrimage that will culminate on October 17 with the annual Arbaeen commemoration.
Arbaeen is one of the world's biggest religious festivals and marks the end of the 40-day mourning period for the seventh-century killing of Imam Hussein by the forces of the Caliph Yazid.
According to Iran's Fars news agency, pilgrims could cross the border unhindered at two other posts further south.
The official IRNA news agency, however, reported that one of them was also closed for several hours on the Iraqi side during the night before reopening.
Around 1.8 million Iranians made the Arbaeen pilgrimage last year, according to official figures.
The death toll from three days of mass protests in Iraq against corruption and unemployment rose to 19 on Thursday, as demonstrations spread to virtually all of the south.
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