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The area was frequented by the Etruscans and, according to some experts, was the place of settlement of Contenebra. Its name has Etruscan origins and comes from the personal name AR (U) LENA.

The Etruscan center was destroyed by the Romans during the conquest of Tuscia and the inhabitants who survived the massacre created two new centers of Arlena and Civitella of Arlena.

In the Middle Ages the people gathered in the vicinity of the village where the castle ruins are visible. The first document that testifies the current town dates from the ninth century.

In the sixteenth century Arlena was included in the Duchy of Castro that Pope Paul III had set up for his son Pier Luigi and his nephew, Cardinal Alessandro Farnese Junior, because he had repopulate this center to cultivate the lands. People came especially from the Umbrian town of Allerona thanks to the allocation of land and tax-exemptions.

With the end of the Duchy, commissioned by Pope Innocent X, Arlena became part of the Apostolic Chamber and in the eighteenth century was given in perpetual lease to Count Alessandro Cardelli. In the nineteenth century, the Apostolic Camera sold it to the Polish Prince Poniatowski.