The old town, Noto Antica, lies 8 kilometres north on Mount Alveria. In 263 BCE the city was granted to Hiero II by the Romans. According to legend, Daedalus stayed in the city after his flight over the Ionian Sea, as did Hercules after his seventh task.

In 866 it was conquered by the Muslims, who elevated the city to become a capital of one of the three districts of the island. In 1091, it became the last Islamic stronghold in Sicily to fall to the Christians. Later it became a rich Norman city.

In the 16th and 17th centuries, the city was home to several notable intellectual figures, including Giovanni Aurispa, jurists Andrea Barbazio and Antonio Corsetto, as well as architect Matteo Carnelivari and composer Mario Capuana. In 1503 King Ferdinand III granted it the title of civitas ingeniosa ("Ingenious City").

In the following centuries, the city expanded, growing beyond its medieval limits, and new buildings, churches and convents were built. The medieval town of Noto was virtually razed by the 1693 Sicilian earthquake. Over half the population is said to have died from the earthquake. The town was rebuilt at the present site, on the left bank of the River Asinaro. These circumstances have led this town to have a unique architectural homogeneity since the core of the town was all built over the next decades after the calamity in what is a typical and highly preserved example of Sicilian baroque. The town was dubbed the "Stone Garden" by Cesare Brandi and is currently listed as a UNESCO World Heritage Site.