The older town, Noto Antica, lies 8 km directly north on Mount Alveria. It was ancient Netum, a city of Sicel origin, left to Hiero II by the Romans by the treaty of 263 BCE and mentioned by Cicero as a foederala citilas , and by Pliny as Latinae conditionis. According to legend, Dedalus stopped here after his flight over the Ionian Sea, as well as Hercules, after his seventh task.

In the Roman era, it opposed praetor Verres. In 866 it was conquered by the Arabs, who elevated to a capital city of one of three districts of the island (the Val di Noto). Later it was a rich Norman city.

In the sixteenth and seventeenth centuries, the city brought forth several notable intellectual figures, including Giovanni Aurispa, jurists Andrea Barbazio and Antonio Corsetto, as well as the architect Matteo Carnelivari: in 1503 king Ferdinand III gave it the title of civitas ingeniosa ("ingenious city"). In the following centuries, the city expanded enlarging its medieval limits; and new buildings, churches and convents were built. These, however, were all totally destroyed by the earthquake of January 11, 1693. The devastation of the city on Mount Alveria was accompanied by its economy, which relied mainly on agricultural products: wine, oil, cereals, rice, cotton and its renowned handicrafts.

The current town, rebuilt after the earthquake on the left bank of River Asinaro, was planned on a grid system by Giovanni Battista Landolina. This new city occupied a position nearer to the Ionian Sea. The presence of architects like Rosario Gagliardi, Francesco Sortino and others, made the new Noto a masterpiece of Sicilian Baroque, dubbed the "Stone Garden" by Cesare Brandi and is currently listed among UNESCO's World Heritage Sites. The new structures are characterized by a soft tufa stone, which under sunlight assumes a typical honey tonality.

The city, which had lost its provincial capital status in 1817, rebelled against the House of Bourbon on May 16, 1860, leaving its gates open to Giuseppe Garibaldi. Five months later, on October 21, a plebiscite sealed the annexation of Noto to Piedmont.

In 1844, Noto was named a bishopric seat, but in 1866 suffered the abolition of the religious guilds, which were deeply linked to the city's structures and buildings.

Noto was freed from fascist dictatorship in July 1943. At the referendum of 1946, the Notinesi people voted in favour of the monarchy.