Sezer arrived on Wednesday. His visit follows calls from the United States for Turkey's help in pressuring Syria to withdraw its troops from Lebanon.
"I hope that [the visit] will help further develop relations between Syria and Turkey, contribute to peace and stability in the region and strengthen the ties between the two peoples," Sezer said before his departure.
The visit is a follow-up to Syrian President Bashar al-Asad's trip to Turkey last year, the first by a Syrian head of state and a symbol of improved ties between the two neighbours.
Sezer's discussions with Syrian leaders could include the two nations' shared concerns about the growing influence of Kurds in Iraq.
There are fears in Syria and Turkey that if Iraqi Kurds were to win independence it could cause unrest among ethnic Kurds in their own countries.
Syrian-Turkish relations were poor for much of the 1980s and 1990s when Turkey accused Syria of harbouring Turkish Kurdish guerrillas.
There was also tension over the construction of Turkish dams that Syria said were restricting the flow of water down the Euphrates and Tigris rivers.
But relations improved after 1998 when Syria, bowing to Turkish pressure, expelled the Turkish Kurdish guerrilla leader Abd Allah Ocalan. The following year Ocalan was captured and imprisoned in Turkey.