In the Roman period the place appears as Natiolum , named in the Tabula Peutingeriana along the ancient Via Litoranea that ran from Capo di Leuca to Ancona and on toward the Veneto — the coastal line on which Bardulos (Barletta), Turenum (Trani), Natiolum and Barium (Bari) follow one another, while Ruvo and Bitonto lie on the inland parallel of the Via Traiana. It may have grown on the ruins of the Peucetian Netium , razed during the Punic wars. Legend prefers a foundation by Perseus, son of Jove, who is said to have landed here and founded Jovis Natio in his father's honour.

For the whole first millennium it was only a village of fishermen, sailors and traders. It was the seat of a Lombard gastaldate from the seventh-century conquest until the Byzantines returned to the Mezzogiorno in the tenth and eleventh centuries.

The walls are the town's other signature. The Arco di Traiano is one of the old gates of the medieval circuit: two ogival arches whose capitals rest on four milestone columns of the Via Traiana — though that road did not in fact pass through the town, and the columns were brought here. The emperor is credited locally with reinforcing the defensive circuit. Later came the Torrione Aragonese , called u tammurre in dialect for its drum-like roundness and visible from the harbour, and the Aragonese walls with the Fortino.

The Concattedrale di Santa Maria Assunta was built from 1113 in Apulian Romanesque with Norman and Eastern elements, on a pre-existing church of Santa Maria dell'Episcopio, and consecrated on 23 May 1283 . A Baroque campaign later remade the interior entirely; what survives of the Romanesque building is the rear facade between its two bell towers — the smaller of them seventeenth-century — part of the presbytery, and the crypt . That crypt, the cemetery and the wall structures beneath the Palazzo Ducale are the physical evidence of the earlier settlement.

One document gives the shape of the old civic order. On 16 July 1522 , Duke Don Ferdinando of Capua received homage from the two mayors of the piazze and from the body of the Universitas . Two piazze means two constituted orders — nobles and people — each with its own mayor, which is worth knowing when reading any pre-1809 municipal document from this town.

From the fifteenth century Giovinazzo traded actively with Venice . But the later centuries went badly: under Angevins, Aragonese and then Bourbons the town declined, and by the eighteenth century it was reduced to about 4,500 inhabitants . Late in that century Ferdinand IV and Maria Carolina visited the cathedral, which stood awkwardly at the far edge of the old town facing the sea.