During the meeting on Wednesday, general Baqeri and President Erdogan also exchanged views on bilateral and defense ties.
Heading a military delegation, the top Iranian general arrived in Ankara on Tuesday morning for talks with top Turkish military and political officials.
Earlier in the day, he held separate meetings with Turkey's President Recep Tayyib Erdogan and Head of National Intelligence Organization (MIT) Hakan Fidan.
The top Iranian general will leave Ankara for Istanbul on Thursday for further meetings with Turkish officials.
Iran and Turkey enjoy cordial bilateral relations. Despite some differences on regional issues, Iran and Turkey are two sides of a trilateral mechanism to maintain ceasefire in certain parts of Syria.
Tehran, Ankara and Moscow cooperation has led to several successful indirect talks between the Syrian government and the opposition groups in the Kazakh capital of Astana.