Sami dates back to the Prehistoric period. The earliest reference to the settlement is found in Homer's writings who described it as part of the kingdom of Ulysses, the leader of Cephallenes. This is the time when the Cephallenes participated in the Trojan War. Traces of organized settlements in the area date back to this period. Vigla Hill was a Mycenean acropolis (the Mycenean period in Greece dates from approximately 1580 to 1100 B.C.).

During the 5th century B.C., Cephalonia was divided into four autonomous, sel-ruled, city states: Krani, Sami, Pronni, and, Palli. The antagonism that existed between these city states is evidenced by the existence of mighty Hellenistic Period acropoles such as the double-hilled Acropolis of Sam (the Hellenistic Period is dated between the 3rd and 2nd centuries B.C.). The remains of this Acropolis show that this was a well organized, flourishing town.

During the 2nd century B.C., Sami's strategic location attracted the interest of the Romans. In 189 B.C., they set out to invade and conquer the island. Sami was the only city state that resisted with determination. The siege was long and relentless, lasting four months. Sami finally surrendered in January 188 B.C. - following the arrival of siege artilery from Amvrakia- suffering extensive plundering. Subsequently, the Romans reorganized the city making it an important connecting point for journeys between Italy and Greece. Archeological remains dating back to this period indicate rigorous construction activity.

Pirate attacks during the 5th and 6th centuries A.C. and destructive earthquakes contributed to the eventual decline and desertion of the city.