It was situated on the ancient coastline below the volcano Vesuvius with nothing to obstruct the view of the sea. It was perhaps owned by Julius Caesar's father-in-law, Lucius Calpurnius Piso Caesoninus. In 1908 CE, Barker suggested that Philodemus may have been the owner.

In 79 CE, the eruption of Mount Vesuvius covered all of Herculaneum with up to 30 metres (98 feet) of volcanic material from pyroclastic flows. Herculaneum was first excavated between 1750 and 1765 CE by Karl Weber by means of tunnels. The villa's name derives from the discovery of its library, the only surviving library from the Graeco-Roman world that exists in its entirety. It contained over 1,800 papyrus scrolls, now carbonised by the heat of the eruption, the "Herculaneum papyri".

Most of the so-called villa of the Papyri still lies unexcavated, however, parts have been cleared of volcanic deposits. Many of the finds are displayed in the Naples National Archaeological Museum. The Getty Villa museum in Malibu, California, is a reproduction of the Villa of the Papyri.

Initially the first papyri scrolls which were obtained in 1752 CE were thrown away due to the high number, then Bernardo Tanucci advised the King to study them. The King subsequently established a commission for the study of the papyri.

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Plan
The villa is located a few hundred metres from the nearest house in Herculaneum. Although it now lies inland, before the volcanic eruption of October 79 CE, the structure occupied more than 250 metres (820 feet) of coastline along the Gulf of Naples. On the other sides it was surrounded by a closed garden, vineyards and woods. The villa had four levels beneath the main floor, arranged in terraces overlooking the sea. It has recently been ascertained that the main floor was 16 meters (52 feet) above sea level in antiquity.

The villa's layout is an expanded version of the traditional Campanian villa suburbana. One entered through the fauces and proceeded to the atrium, which functioned as an entrance hall and a means of communication with the various parts of the house. The entrance opened with a columned portico on the sea side.

After passing through the tablinum, one arrived at the first peristyle, made up of ten columns on each side, with a swimming pool in the centre. In this area were found the bronze herm adapted from the Doryphorus of Polykleitos and the herm of an Amazon made by Apollonios son of Archias of Athens. The large second peristyle could be reached by passing through a large tablinum in which, under a propylaeum, was the archaic statue of Athena Promachos. A collection of bronze busts were in the interior of the tablinum. These included the head of Scipio Africanus.

The living and reception quarters were grouped around the porticoes and terraces, giving occupants ample sunlight and a view of the countryside and sea. In the living quarters, bath installations were brought to light, and the library of rolled and carbonised papyri placed inside wooden capsae, some of them on ordinary wooden shelves and around the walls and some on the two sides of a set of shelves in the middle of the room.

The grounds included a large area of covered and uncovered gardens for walks in the shade or in the warmth of the sun. The gardens included a gallery of busts, hermae and small marble and bronze statues. These were laid out between columns amid the open part of the garden and on the edges of the large swimming bath.

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The Villa of the Papyri was discovered in 1750 by farmers when digging a well. The following excavation work was conducted first by Roque Joaquín de Alcubierre and later by the Swiss engineer Karl Jakob Weber, who worked under Alcubierre for King Charles VII of Naples.

Camillo Paderni who took part at the excavations and was possibly the first to transcribe papyri, noted in a letter dated 1754, "...in five places, where we might have expected to meet with busts or statues, the antients had been digging before us, and taken them away. The method, whereby they regulated their searches, seems to have been this: where the ground was pretty easy to work, they dug through it and where they met with the solid lava they desisted. But whether they were in want of money, or of hands, they certainly did not perfect their intention; as is plain from the statues, which we have found".

Excavations were halted in 1765 due to complaints from the residents living above. The exact location of the villa was then lost for two centuries. In the 1980s work on re-discovering the villa began by studying 18th century documentation on entrances to the tunnels and in 1986 the breakthrough was made through an ancient well. The backfill from some of the tunnels was cleared to allow re-exploration of the villa when it was found that the parts of the villa that survived the earlier excavations were still remarkable in quantity and quality.

Excavation to expose part of the villa was done in the 1990s and revealed two previously undiscovered lower floors to the villa with frescoes in situ. These were found along the southwest-facing terrace of about 4 metres height. The first row of rooms lying below the arcade was evidenced by a series of rectangular openings along the façade. Limited excavations recommenced at the site in 2007 to preserve the remains when carved parts of wood and ivory furniture were discovered. Since then limited public access became available.

As of 2012, there were still 2,800 m2 left to be excavated of the villa. The remainder of the site has not been excavated because the Italian government is preferring conservation to excavation, and protecting what has already been uncovered. David Woodley Packard, who has funded conservation work at Herculaneum through his Packard Humanities Institute, has said that he is likely to be able to fund excavation of the Villa of the Papyri when the authorities agree to it; but no work will be permitted on the site until the completion of a feasibility report, which has been in preparation for some years. The first part of the report emerged in 2008 but included no timetable or cost projections, since the decision for further excavation is a political one. Politics involve excavation under inhabited areas in addition to unspecified but reported references to mafia involvement.

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Frescoes included, Theseus victorious over the Minotaur, Telephus suckled by the hind, Chiron teaching Achilles the lyre, Perseus slaying Medusa, a charioteer, and papyri.

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J. Paul Getty Museum
In 1970, oil billionaire J. Paul Getty engaged the architectural firm of Langdon and Wilson to create a replica of the Villa dei Papiri to serve as a museum where his collection of antiquities would be displayed. Based on Weber's plans published in Le Antichità di Ercolano, the museum was built on Getty's Malibu ranch in 1972–1974. Architectural consultant Norman Neuerburg and the curator of Getty's antiquities, Jiří Frel, worked closely with Getty and the architects to ensure the accuracy of the museum building's design .

Since the Villa dei Papiri was unexcavated, Neuerburg based many of the villa's architectural and landscaping details on elements from other ancient Roman houses in the towns of Pompeii, Herculaneum, and Stabiae. For example, the mosaic fountain in the museum's garden peristyle replicates the one in the Nymphaeum of the House of the Large Fountain at Pompeii. In 1997, the Getty Museum was relocated to the Getty Center. The Malibu villa was renovated and reopened in 2006. The reconceived Getty Villa, as it is now called, serves as an annex dedicated to the display of the museum's antiquities and as a centre for the study of ancient art.