Sheikh Tamim will hold talks on "bilateral ties and regional issues as well as global developments", Turkey's presidential office said in a statement.
The two leaders met at the presidential complex in the capital Ankara, Turkish presidential sources said.
The Emir was welcomed on arrival at Esenboga International Airport by Turkish Deputy Prime Minister for Economic Affairs Mehmet Simsek, Governor of Ankara Ercan Topaca and Qatar's Ambassador to Turkey Salem bin Mubarak Al Shafi in addition to senior officials and members of the Qatari Embassy.
They were also joined in the two-and-half hour meeting by Energy Minister and Erdogan's son-in-law Berat Albayrak, images showed.
Erdogan has been a major supporter of Doha since June 5, when Saudi Arabia, Bahrain, the United Arab Emirates, and Egypt cut ties and blockaded Qatar, accusing it of supporting "terrorism" and fostering ties with their rival Iran.
Saudi Arabia, the UAE, Egypt and Bahrain cut diplomatic and trade links with Qatar on June 5, suspending air and shipping routes with the world's biggest exporter of liquefied natural gas, which is home to the region's biggest US military base.
Qatar emir to visit Turkey Thursday: Turkish presidency
Doha, however, denies the claims and Ankara has insisted there is absolutely no evidence to back the allegations.
The four Arab states calling to fight terror have reiterated that the measures that they have taken against Qatar are legitimate sovereign decisions that are by no means a "siege" but a boycott resulting from the damage caused by the irresponsible actions of Doha through its support, financing and harboring of terrorism and terrorist groups, the Saudi Press Agency (SPA) reported.
Erdogan in July embarked on a regional tour of the Gulf countries, with visits to Saudi Arabia, Kuwait and Qatar in a bid to defuse the crisis.
After visiting Turkey, the emir is due to visit Berlin on Friday for talks with German Chancellor Angela Merkel, his first trip to a western capital since the crisis began.
"Turkey gave a clear message that they [the Saudi-led bloc] must give up the idea of a military operation against Qatar by sending troops and military equipment".