During the break-up of the Roman empire, Gaeta, like Amalfi and Naples, would seem to have established itself as a practically independent port and to have carried on a thriving trade with the Levant. Its history, however, is obscure until, in 823, it appears as a lordship ruled by hereditary Itypati or consuls.

In 844 the town fell into the hands of the Arabs, but four years later they were driven out with help supplied by Pope Leo IV and was given to the count of Capua as a fief of the Holy See. In 877, however, the hypatus John (Joannes) II succeeded in recovering the lordship, which he established as a duchy under the suzerainty of the East Roman emperors. In the 11th century the duchy fell into the hands of the Norman counts of Aversa, afterwards princes of Capua, and in 1135 it was definitively annexed to his kingdom by Roger of Sicily.

In military history the town has played a conspicuous part. Its fortifications date back to Roman times, and a first-century mausoleum of the Roman general Lucius Munatius Plancus stands atop the Split Mountain. These fortifications were extended and strengthened in the 15th century, and indeed throughout the history of the Kingdom of Naples (later the Two Sicilies).

In the following centuries Gaeta was sieged and stormed by the Austrians, in 1734 by French, Spanish and Sardinian troops under the future King Charles of Naples, in 1806 by the French, in 1815 by the Austrians.

In November 1848 Pope Pius IX, after his flight in disguise from Rome, found a refuge at Gaeta, where he remained until September 4, 1849. Finally, in 1860, it was the scene of the last stand of Francis II of the Two Sicilies against the forces of United Italy. Shut up in the fortress with 12,000 men, after Garibaldi's occupation of Naples, the king offered a stubborn resistance, and it was not till February 13, 1861 that, the withdrawal of the French fleet having made bombardment from the sea possible, he was forced to capitulate.

During World War II, the city retained its strategic importance for Mussolini and later for his Nazi allies. After the king dismissed Mussolini, the latter was initially taken via Gaeta to the island prison of Ponza (where Mussolini had previously locked up many of his political enemies). To keep the population ignorant of the massive convoy, a false air-raid siren sounded. (Mussolini would later be transferred to Gran Sasso, from where the Germans rescued him.)

After Italy surrendered to the Allies, however, the town's fortunes began to decline. Recognizing the city's strategic importance, and fearful of an Allied landing in the area, German troops occupied the city and expelled most of the population. The zone of exclusion began with a five-kilometer border from the historical city center; soon after, however, the population was expelled even beyond this point. The Gaetani were finally ordered to leave the area completely; those who could not were placed in a concentration camp, and a few were taken to Germany.

Following the Allied advance across the Garigliano and the Allied occupation of Rome, the Gaetani were allowed to return to their city and begin the process of rebuilding. However, the decades since World War II have been as difficult for Gaeta as they have been for most of Italy's southern regions. Its importance as a seaport has nearly vanished in favor of the nearby town of Formia. Today NATO maintains a base of operations at Gaeta. More recently, the city has turned to summer tourism and to specialized agricultural products, namely its tomatoes and olives.

The Gaetani speak a dialect of Italian that, while similar to the nearby Neapolitan, is one of the few Italian dialects to preserve Latin's neuter gender. Distinctive local cuisine includes the tiella, which resembles both a pizza and a calzone. The town is also notable for its splendid beaches (Serapo, Fontania, Sant'Agostino), and its distinctive brand of olives, marketed throughout the world. Gaeta has erected a monument to Giovanni Caboto (John Cabot), who according to many was born there (although other sources give Genoa).