Inhabited since the Bronze Age, the name probably derives from the local oak forests (quercus robur farnia).
The noble "Farnese" family was first mentioned in a 14th century document. The family dominated the local area until 1825, when Farnese fell under the control of the Papal State. In 1834 it was bought by the French Marquis De Gourmont and then Alessandro Torlonia.

The old town centre dates back to the 11th-12th Centuries and was built on a natural outcrop of Tuff rock.
On 19th October 1867 there was a battle between Garibaldi's Red Shirts and the Papal army. Some 300 volunteers (mostly from just over the Tuscan border) fought for 3 hours. There is a plaque comemmorating the death of the French General Duphornel on the facade of Palazzo Luccattini (just past the cemetery), plus a memorial to 3 Tuscan soldiers.