The President, who was accompanied by Interior Minister Rehman Malik and Petroleum Minister Dr Asim Hussain, was received at Mehrabad Airport by Iranian Petroleum Minister Mohammad Aliabadi.
Pakistan's Ambassador in Iran and senior embassy officials were also present on the occasion.
Zardari will hold talks with his counterpart President Mahmoud Ahmadinejad and supreme leader Ali Khamenei.
Iranian officials have given few details of the talks' agenda. Iran's ambassador to Pakistan Mashala Shokri said only that they would address "bilateral relations and regional issues."
But the visit comes less than a month after Zardari was in Tehran for a counter-terrorism summit on the sidelines of which Iran and Pakistan agreed to cooperate with Afghanistan in the fight against militants.
Zardari's visit also comes after Washington announced it was deferring $800 million in military aid to Islamabad while it sought better defence cooperation.
The United States suspended the military assistance, about one third of its $2.7 billion annual defence package, some two months after a US operation killed al Qaeda leader Osama bin Laden in Abbottabad.
After the raid, the United States pledged to keep relations steady with Pakistan. But US frustration has mounted, including over Islamabad's decision to oust up to 200 US personnel who planned to train Pakistani forces.
Iranian officials have been vocal in their criticism of the prolonged US troop deployments in neighbouring Afghanistan and Iraq, both of which are now set to be drawn down.
They have also repeatedly accused the US and Pakistani intelligence services of helping insurgents active in Iran's southeastern province of Sistan-Balochistan, which borders Pakistan's own restive Balochistan province.
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