"The ground should be prepared for holding an absolutely free election with no preconditions," Rouhani told visiting Iraqi Prime Minister Nuri al-Maliki, the presidency website reported.
Rouhani, whose country backs Syrian President Bashar al-Assad, said the conference should also aim for the "complete expulsion of the terrorists from Syria," using the regime's term for its foes.
"It is our mutual responsibility to defend the ideals and demands of the Syrian nation in all international conferences," especially at the so-called Geneva 2, he said.
The government in Damascus, meanwhile, has said Assad will remain president and lead any transition agreed at the conference scheduled for January 22.
The opposition and rebels fighting the regime reject the participation of Iran at the conference and insist Assad play no role in a transition.
At his meeting with Rouhani, Maliki hailed the nuclear deal between Iran and world powers in late November, saying it will contribute to the region's stability.
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