The first traces of human settlement in the area date back to the Late Bronze Age and to the Etruscans, who were also present along the coast and further inland, as shown by the Necropolis of Poggio Tondo. In Roman times, the area of Puntone – where the marina stands today – saw the development of the port of Portus Scabris, an important crossroads for goods moving across the Mediterranean.

As for the town itself, its current layout and many of its surviving buildings largely date to the Middle Ages, when Scarlino was first under the rule of the Aldobrandeschi family, later passed to the Municipality of Pisa, and eventually to the Appiani family, becoming part of the State of Piombino.

In the 19th century, Scarlino played a role in the Risorgimento: immediately after the First War of Independence, Giuseppe Garibaldi embarked from Cala Martina, heading for Portovenere.

At the turn of the 20th century, the Bandite promontory, with the Terra Rossa mining port, became an important hub for the trade of pyrite extracted in the Metalliferous Hills. The chemical industry that once processed pyrite still exists near the Padule, a wetland area now protected for its ecological value.