An ancient port formed by small parallel basins capable of accommodating single vessels was still visible at the end of the 19th century near Forte Michelangelo.

The nearby monumental baths at Terme Taurine were built originally in the Roman Republican era, possibly by Titus Statilius Taurus, prefect of Rome.

Trajan's sumptuous villa pulcherrima (most beautiful, according to Pliny[3]) must have been built at the same time but traces have yet to be found, although the Terme Taurine baths and the large cistern nearby are likely to have been included.

[7] Inscriptions from between the 2nd and 3rd centuries from a cemetery near the Roman harbour prove the presence of classiari, sailors from the navy, and also of a noble class.

As the port was raided by the Saracens in 813–814, 828, 846 and finally in 876, a new settlement in a more secure place was therefore built by order of Pope Leo IV as soon as 854.

[4] The Popes gave the settlement as a fief to several local lords, including the Count Ranieri of Civitacastellana and the Abbey of Farfa, and the Di Vico, who held Centumcellae in 1431.

In that year, pope Eugene IV sent an army under cardinal Giovanni Vitelleschi and several condottieri (Niccolò Fortebraccio, Ranuccio Farnese and Menicuccio dell'Aquila among them) to recapture the place, which, after the payment of 4,000 florins, became thenceforth a full Papal possession, led by a vicar and a treasurer.

During World War II, the Allies launched several bombing raids against Civitavecchia, which damaged the city and inflicted several civilian casualties.

[14] On June 27, 1944, two American soldiers from the 379th Port Battalion, Fred A. McMurray and Louis Till, allegedly raped two Italian women in Civitavecchia and murdered a third.

[15] Civitavecchia is today a major cruise and ferry port, the main starting point for sea connection from central Italy to Sardinia, Sicily, Tunis and Barcelona.

[18] The massive Forte Michelangelo was first commissioned from Donato Bramante by Pope Julius II, to defend the port of Rome.

Pius IV added a convict prison, and the arsenal, designed by Bernini, was built by Alexander VII.

The town is also interested by a project regarding a new motorway, the Civitavecchia-Venice or New Romea,[24] nowadays completed as a dual carriageway between Viterbo and Ravenna (via Terni, Perugia and Cesena) and commonly known in Italy as the Orte-Ravenna.