The territory, as shown by archeological excavations, was inhabited by the Samnites, defeated by the Romans in a battle near Aquilonia in 293 BC. Under the Lombards the population lived in a number of "casali" to join finally in one center, called Carbonara (Carunar in the local dialect) since the main occupation of the inhabitants was that of charcoal makers. In the Middle Ages, it was called Carbonara, probably due to the presence in its territory of stones containing petroleum, which burned with live flame like coals. After the unity of Italy the name was changed again to the ancient Aquilonia.

On the night of 23 July 1930 the ruinous Vulture earthquake almost completely destroyed the town, with a heavy toll of 231 dead and over one thousand wounded. The old town was abandoned, and with funds from the government a new town was built in a higher position, in an area called Contrada Malepasso: in just 90 days almost one hundred small houses were built. Nowadays on the spot where Aquilonia rose before the earthquake a restoration has been started so as to make a Parco Archeologico in the area. The project will also be based on old photographs of the town, and on donations by private families of what they could salvage after the destruction.