The Prehistoric Collection grew out of the discoveries of the great pioneering excavations of the late nineteenth century, which gave form and title to the civilizations of Greek prehistory.

Two passionate men laid the foundations for the development of Greek prehistoric archaeology. Charismatic and ambitious, Heinrich Schliemann (1822-1890) excavated legendary places like Troy, Mycenae and Tiryns. Christos Tsountas (1857-1934) carried on the Mycenae excavations, dug the famous Vapheio tholos tomb and delved even deeper in time with his explorations in the Cycladic islands and Thessaly, which revealed the first civilizations in Greece. Tsountas initiated the first systematic investigations in Greece, which set the standard for research into the Neolithic, Cycladic and Mycenaean civilizations. As Keeper of the Mycenaean and Egyptian Collections of the Museum, from 1896 to 1904, he was responsible for the first inventory of the Prehistoric Collection, which was moved to the newly established National Archaeological Museum in 1892.

In that same year Sophia Schliemann, wife of Heinrich Schliemann, donated his personal collection of Trojan antiquities to the new museum. The finds of Greek and foreign archaeologists during the twentieth century enriched the Prehistoric Collection with priceless works from all over Greece. Exhibits from the Peloponnese, Attica, Thessaly and the Cyclades make up the body of the Collection,while important works also come from Lemnos, Lefkada, Kythera and Skopelos.

With the growth of local museums after the Second World War, the input of new finds to the Prehistoric Collection gradually dwindled and in the 1970s, after the transport of the famous wall-paintings from Akrotiri in Thera, practically stopped. New exhibits have enriched the collection inrecent years thanks to the crack down by Greek authorities on the illicit antiquities trade and their confiscation of unexpected finds such as the gold jewelry of the 'Neolithic Treasure' in 1997.