A total of 63 children from Greece's northeastern Komotini and Xanthi provinces are to participate in the program run by Turkey's top religious authority, known as Diyanet.
The children will also be able to visit historic sites in such Turkish cities as Edirne, Istanbul or Bursa, Anadolu Agency reported.
On the first day of the program on Tuesday, the pupils met Edirne mufti (top provincial Muslim cleric) Emrullah Uzum.
Speaking to reporters, Uzum said they would provide religious education to the children, as well as provide information about Turkish culture.
The Western Thrace region of Greece is home to a Turkish Muslim minority of around 150,000 people.