The crag was settled long before anyone wrote its name down — finds run back to prehistory. Which ancient town stood here is still argued: scholars point to two neighbouring or overlapping Sicanian settlements, Hybla Gereatis and Inessa . The identification with Hybla rests on an inscribed altar consecrated to the goddess Hyblaia found in the area. It is a reasonable reading rather than a settled one, and the argument has run for two centuries.

In the Roman period the district supplied grain and timber for the imperial fleet. Byzantine rule followed, then Arab from the ninth century, when the place was called Batarnù . Paternò was among the least Islamised parts of Sicily — its population predominantly indigenous and Byzantine Christian — which is why the Norman advance found it easy ground and why Roger I d'Altavilla , having taken the area around 1061 , chose to quarter here.

In 1072 Roger raised it to a county and built the donjon. Together with the towers at Adrano and Motta Sant'Anastasia it was designed to squeeze Muslim Catania — ad infestandam Catanam — rather than merely to defend. The tower is lava ashlar, three floors, some 34 metres high, walls 2.6 metres thick with the stairs cut inside them, and it is oriented to the cardinal points. A few sources credit its construction to Roger II; the contemporary chronicler Geoffrey Malaterra and the comune both name the Great Count, Roger I.

It was a residence as much as a fortress. Frederick II of Swabia lived here in 1221–1223 ; Queen Eleonora of Aragon and Queen Bianca of Navarre afterward; and under the Bourbons parts of it served as a public prison.

Under the Aragonese the town was a royal demesne, except when it was held as a county by the Alagona. In 1456 it passed by purchase to the Moncada , counts of Adrano, who were raised to a principality in 1565 and held Paternò until feudalism was abolished in the Kingdom of Sicily in 1812 . Four centuries under one house is the frame for almost all the town's surviving pre-1820 documentation.