The first official evidence of the existence of a housing cluster comes from a document dated 7th February 1252 in which it mentions Castrum Montis Compatris, a deed of separate property ownerships between Oddone and Giordano Colonna.

Actually, there are already more ancient traces dating back to the year 1090. Furthermore, tradition tells of the Hermitage of San Francesco in a grotto along the west side slopes of the hill where the present hermitage stands, which up to a few years ago was a cemetery.

It seems that, enchanted by the splendid and peaceful nature, San Francesco suggested it to three of his brothers, who built a small convent there, the ruins of which are still visible today.

One of the brothers from this small convent, Beato Pietro (Saint Peter) from Monte Compatri is still worshipped today at Oviedo, in Spain.

The town was first owned by the Counts of Tusculum and then purchased by the Annibaldi, relatives of Innocent III; in 1423 it belonged to the Colonna who built a castle that is now buried under the new buildings; in 1582 it was handed over to Marco Altemps, nephew of Pope Pius IV, who built a palace near the cathedral; last in 1613, it was given by Gian Angelo Altemps to Cardinal Scipione Borghese.

The Borghese family were the landlords of Monte Compatri for about 200 years (from 1613 to 1815), which were years of splendour and prosperity. Scipione was a well known patron and a great lover of classical art, under which the town flourished. It became a Principality, yet maintaining its local independent administration and was chosen by the cardinal as his summer residence.

During the Roman Republic, Monte Compatri was land of conflict between Garibaldi and the Bourbon soldiers. After the feudalism had come to an end in the Lazio region, the territory was given back to the Church. In 1870, when Rome became part of the Kingdom of Italy, and the temporal power of the Vatican State ended, the church was obliged to return the extra-urban fiefs that organized themselves in independent municipal units of the Kingdom of Italy. Monte Compatri became a town in 1874.

During the Second World War, Monte Compatri had suffered enemy occupation, bombings and destruction. The signs of these conflicts were visible on the buildings up to a few years ago and the people today still remember from that time, Mario Intreccialagli and Placido Martini, two martyrs of the Fosse Ardeatina. At Monte Compatri a street has been named to each of them in remembrance.