Mottaki will discuss Iran-Turkey bilateral relations as well as regional issues during the visit, the official news agency IRNA quoted an Iranian embassy official in Turkey as saying.
Mottaki travelled to Baghdad on Wednesday to meet and hold talks with Iraqi officials.
Turkish Foreign Minister Ali Babacan visited Tehran earlier this week.
Mottaki has made at least four other trips to Turkey since becoming Foreign Minister.
Mottaki has a chequered history in Turkey and was once expelled for his involvement in terrorism when he was the Islamic Republics ambassador to Ankara.
He has been accused of involvement in a series of terrorist attacks in Turkey in the late 1980s, according to Iranian exiles and defectors from the theocratic regime.
Turkish authorities had asked him to leave the country in 1989, when he was Irans ambassador in Ankara, after his role in several terrorist incidents in Turkey became known.
As a radical Islamist in his student days in Indias Bangalore University, Mottaki was a fervent supporter of Ayatollah Ruhollah Khomeini. He returned to Iran during the revolution and joined the ranks of the Islamic Revolutionary Guards Corps (IRGC) soon after the fall of the Shahs regime in 1979. After taking part in the bloody campaign against Kurdish dissidents, Mottaki moved to the Foreign Ministry, where for some time he was the IRGC liaison officer.
Mottaki was appointed Irans ambassador to Turkey in 1985 and it was during his tenure in Ankara that the Revolutionary Guard-turned-diplomat became involved in a number of terror attacks and assassinations of dissidents, according to Iranian opposition figures and defectors. In the 1980s and the early 1990s, at least 50 Iranian dissidents were kidnapped or assassinated in Turkey by Iranian secret agents often working closely with diplomats from Irans embassy and consulates.
On Mottakis watch, the Iranian embassy in Ankara and the consulate-general in Istanbul were turned into safe houses for agents of Irans notorious secret police hunting down Iranian dissidents, according to exiles.
The Turkish authorities ordered Mottaki to leave Turkey in October 1989 for his role in assassinations and kidnappings in that country. The expulsion was couched in diplomatic terms, and Turkey agreed to allow Iran to avoid public embarrassment by withdrawing its ambassador.
Mottaki later became Vice-president of Islamic Cultural and Communications Organisation, an agency created by Supreme Leader Ayatollah Ali Khamenei for export of the Islamic revolution to other parts of the Muslim world.
