In 1933 two sets of gold and silver plates recording in the three forms of cuneiform—Ancient Persian, Elamite, and Babylonian—the boundaries of the Persian empire were discovered in the foundations of Darius's hall of audience. A number of inscriptions, cut in stone, of Darius I, Xerxes I, and Artaxerxes III indicate to which monarch the various buildings were attributed. The oldest of these on the south retaining wall gives Darius's famous prayer for his people: “God protect this country from foe, famine, and falsehood.” There are numerous reliefs of Persian, Median, and Elamite officials, and 23 scenes separated by cypress trees depict representatives from the remote parts of the empire who, led by a Persian or a Mede, made appropriate offerings to the king at the national festival of the vernal equinox.

Behind Persepolis are three sepulchres hewn out of the mountainside; the facades, one of which is incomplete, are richly ornamented with reliefs. About 8 miles (13 km) north by northeast, on the opposite side of the Pulvār River, rises a perpendicular wall of rock in which four similar tombs are cut at a considerable height from the bottom of the valley. This place is called Naqsh-e Rostam (“Picture of Rostam”), from the Sāsānian carvings below the tombs, which were thought to represent the mythical hero Rostam. That the occupants of these seven tombs were Achaemenian kings might be inferred from the sculptures, and one of those at Naqsh-e Rostam is expressly declared in its inscriptions to be the tomb of Darius I, son of Hystaspes, whose grave, according to the Greek historian Ctesias, was in a cliff face that could be reached only by means of an apparatus of ropes. The three other tombs at Naqsh-e Rostam are probably those of Xerxes I, Artaxerxes I, and Darius II (Darius II Ochus) (Ochus). The two completed graves behind Persepolis probably belong to Artaxerxes II and Artaxerxes III. The unfinished one might be that of Arses, who reigned at the longest two years, but is more likely that of Darius III, last of the Achaemenian line, who was overthrown by Alexander the Great.

At the foot of Naqsh-e Rostam, situated in the direction of the cliff face, rests a square building known as Kaʿbeh-ye Zardusht (“Kaaba of Zoroaster”). The building, which is roughly 40 feet (12 metres) high and 24 feet (7 metres) square, probably was constructed in the first half of the 6th century BCE, although it has numerous inscriptions from later periods. Though the building is of great linguistic interest, its original purpose is not clear. It may have been a tomb for Achaemenian royalty or some sort of altar, perhaps to the goddess Anahiti (Anāhiti).

Though archaeologists have discovered evidence of prehistoric settlement, inscriptions indicate that construction of the city began under Darius I, who, as a member of a new branch of the royal house, made Persepolis the capital of Persia proper, replacing Pasargadae, the burial place of Cyrus II (the Great). Built in a remote and mountainous region, Persepolis was an inconvenient royal residence, visited mainly in the spring. The effective administration of the Achaemenian realms was carried on from the imperial cities of Susa, Babylon, and Ecbatana. This accounts for the Greeks being unacquainted with Persepolis until Alexander the Great's (Alexander the Great) invasion of Asia. In 330 BCE, during the reign of Darius III, Alexander plundered the city and burned the palace of Xerxes (Xerxes I), whose brutal campaign to invade Greece more than a century before had led, eventually, to Alexander's conquest of the Persian empire. In 316 BCE Persepolis was still the capital of Persis as a province of the Macedonian empire. The city gradually declined under the Seleucid kingdom and after, its ruins attesting its ancient glory.

About 200 CE the nearby city of Istakhr (Estakhr, Stakhr) was the seat of local government, and Istakhr acquired importance as a centre of priestly wisdom and orthodoxy. Thereafter the city became the centre of the Persian Sāsānian dynasty, though the stone ruins that still stand just west of Persepolis suggest that Istakhr dates from Achaemenian times. The Sāsānian kings (3rd–7th century CE) covered the face of the rocks in that neighbourhood—and in part even the Achaemenian ruins—with their sculptures and inscriptions in Pahlavi and must themselves have built largely at Persepolis, though never on the same scale of magnificence as that of their ancient predecessors. The Romans knew as little about Istakhr as the Greeks had about Persepolis, in spite of the fact that for 400 years the Sāsānians maintained relations, friendly or hostile, with the Roman Empire.

At the time of the Arab conquest, Istakhr offered a desperate resistance. The city was still a place of considerable importance in the first century of Islam, although its greatness was soon to be eclipsed by the new metropolis of Shīrāz. By the 10th century CE it had become an insignificant place, as may be seen from a description of it written by the Arab geographer al-Maqdisī (Maqdisī, al-) (c. 985). In the mid-11th century the Seljuq emir Qutulmish razed it and transferred its population to Shīrāz.