In the Division of Protohistory and Near Eastern Archaeology, courses primarily focus on the prehistoric periods of Anatolia, Mesopotamia, and Iran. These courses cover the Paleolithic period, where the first cultural materials of humanity emerged, and extend to the Neolithic, Chalcolithic, Bronze, and Iron Ages.

Protohistory and Near Eastern Archaeology delve into the period of human history starting from the Neolithic Age (approximately mid-10,000 BCE), which marks the beginning of agriculture and the emergence of the first settled life. The course spans sequentially through the Chalcolithic Age (5000–3000 BCE), Bronze Age (3000–1200 BCE), and the Iron Age (1000–500 BCE), covering cultures and civilizations that spread throughout the entire Anatolia and the broader region of Anatolia (mainland  Greece and the Aegean Islands, Crete, Cyprus, the Balkans, Caucasus, Iran, Mesopotamia, Syria, Palestine, Egypt). It investigates the significant cultural developments and civilizations during this period, which is crucial in human history, marking the transition to settled life and the discovery of writing, leading to the onset of the first historical ages. In addition to providing a cultural history, the courses thoroughly examine the topics with visual materials to enhance understanding.