The meeting with the Iranian president was held behind closed doors, but the regime's nuclear programme and the Syrian crisis are believed to be among the issues discussed between the two leaders.
During a two-day visit to the Iranian capital, Erdogan also met with other senior officials, including the vice president, Mohammad Reza Rahimi, and the parliamentary speaker, Ali Larijani.
Iranian media reported that Erdogan spoke against pressure on countries with peaceful nuclear activities in a joint press conference with Rahimi.
"Nobody has the right to oppose peaceful nuclear activities, and Turkey is against any pressure over peaceful nuclear activities," Iran's English-language newspaper, Tehran Times, quoted Erdogan as saying. "Any wise person is against nuclear weapons and approves of the use of nuclear energy for peaceful purposes."
Iran's foreign minister, Ali Akbar Salehi, announced on Wednesday that fresh nuclear talks with the world's major powers, including the US, France, Germany, China, Russia and Britain - the group known as P5+1 - were expected to be held on 13 April, although a venue for the negotiations has not yet been designated.
"We had made a proposal to hold the nuclear meeting in Istanbul. The Iranian foreign minister had expressed a desire to hold the nuclear negotiations in Istanbul. We are waiting for the decision of the P5+1," Erdogan said in quotes carried by the Turkish newspaper, Hurriyet Daily News.
Before his Tehran visit, Erdogan was in South Korea, where he took part in a nuclear security summit and held talks with US president, Barack Obama. That has led to speculations that the Turkish leader is playing a mediatory role between Tehran and the west over the regime's nuclear standoff.
The Turkish newspaper Zamanreported on Thursday the venue for the future talks is still unclear and that the P5+1 is more willing to hold the negotiations in a European capital than in Turkey.
Iran and Turkey are close allies in the Middle East but hold opposite views on Syria. Little is known about Erdogan's negotiations with Iranian officials about the Syrian crisis, but Turkish media reports saidt he was due to press Iran on its support for the Assad regime.
Many analysts, however, are sceptical about the outcome of the Turkish leader's negotiations with Iran over Syria. Writing in the Hurriyet Daily News, Turkish journalist Mehmet Ali Birand said a change in Iran's stance on Syria was impossible.
In the mid or long term, the fall of al-Assad would cause Iran to lose its influence in the region to a great extent. It would also lose its influence in Lebanon and it would be impossible for the 'Shiite corridor', which it is trying to form through alliances with Syria and Iraq, to access to the Mediterranean
Saledi had announced yesterday that the UN/Arab League peace envoy, Kofi Annan, was scheduled to visit Tehran for talks on Syria next week but a spokesman for the former UN secretary general has denied the remarks made by the Iranian foreign minister.