Until the early Middle Ages the town's history is the history of Sarcapos, a trading city that stood near the mouth of the Flumendosa and was the only river port on the whole eastern coast of Sardinia, a support point on the routes towards Etruria. It appears in the Roman itineraries along the road from Cagliari to Olbia, between Ferraria and Porticenses, near the mouth of the Saipros Potamos, that is the Flumendosa. From the eighth century, because of raids, the inhabitants moved to where Villaputzu stands today, easier to defend. Medieval documents call the village in many ways — Villa Pupus, Villa Pubussi de Sarrabus, and then Pututhi, Pupusti, Pupucci between 1316 and 1346. In its territory the judges of Cagliari had a castle, that of Quirra. With the Aragonese conquest, in 1324, the village broke into two settlements, Tarruti and Villa Pupusi; the castle was besieged in vain by the Doria and then by the men of Arborea, and in 1363 Peter the Fourth the Ceremonious ceded it to Berengario Carroz along with the village: Villaputzu thus entered the county of Quirra with another seventy-seven villages, some of which no longer exist.
In 1646 a French warship was wrecked on this shore: four hundred of the crew got ashore and fortified themselves inside the castle, but had to surrender and were taken prisoner; the artillery salvaged from the ship was carried to Cagliari and used to defend the city's bastions. The town was redeemed from its last feudal lords, the Osorio de la Cueva, marquises of Quirra, in 1839. The old church of San Giorgio, built by the Genoese in the twelfth century and rebuilt by the Aragonese in late Gothic style, collapsed in the twentieth century through neglect: which is why in 1904 the bishop of Ogliastra Giuseppe Paderi Concas, a native of the place, dedicated the parish church to the patron saint, when until then it had borne the name of Santa Caterina. Since 1956 part of the territory has housed the inter-force experimental range of Salto di Quirra, and a trial is under way to establish responsibility for the impact that more than half a century of weapons testing has had on the health of workers and of those who live and farm in the neighbouring lands. From Villaputzu came Efisio Melis, born in 1890 and dead at Cagliari in 1970, one of the great players of the launeddas: in the village his admirers were set against those of another fine player, Antonio Lara.