Rouhani's first official visit to Russia comes as the two backers of the Syrian regime push for ways to end the six-year conflict in the country, having done much to marginalise US influence in peace talks.
At the start of their meeting, Putin told Rouhani that Moscow and Tehran "work very effectively, practically on all fronts, in international action and the resolution of major and very grave international problems," state television showed.
Iranian foreign ministry spokesman Bahram Ghasemi said ahead of Rouhani's trip that the leaders would discuss "regional issues especially the Syrian crisis, solutions to end it quickly," as well as ways to counter "terrorism and extremism".
Moscow has formed an unlikely alliance with Ankara since 2016, envisioning Turkey as part of a solution to the Syrian conflict.
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But Iran has been more wary about Turkey's involvement in efforts to end hostilities, with tensions mounting after Moscow and Ankara left Tehran out of a truce they brokered in December.
Rouhani -- accompanied by Foreign Minister Mohammad Javad Zarif, Oil Minister Bijan Zanganeh and other high-ranking officials -- is expected to sign a slew of economic cooperation agreements with Russia, according to Iranian state media.
It said that a "variety of bilateral documents" would be signed at the end of the meeting but did not specify in which fields.
Kremlin spokesman Dmitry Peskov said earlier Tuesday that Moscow was striving to bolster its relations with Tehran, which he said had "very solid potential".
After arriving on Monday, Rouhani met Prime Minister Dmitry Medvedev, with the Iranian president saying he hoped his visit would mark a "new turning point" in relations, Russian state media reported.
Russia is to build nine of Iran's 20 proposed nuclear reactors and has emerged as a long-term arms partner, supplying Tehran with its S-300 air defence missile system.
The relationship has blossomed under Rouhani despite the countries having a complicated history over territory, oil and Communist ideology.