Persian religion is still the subject of debate among experts although there is much evidence that the rulers at least were Zoroastrian. This is the religion named after the prophet Zarathushtra, known by the Greeks as Zoroaster. Its followers worship one great god, Ahura Mazda, and 'helper' gods such as Mithra (the sun god) and Anahita (the 'goddess of all waters').

Ahura Mazda seems to have been represented in Achaemenid art by the winged disc with a human figure holding a ring or flower. He is described in inscriptions by the kings as 'the great god' or 'the greatest of gods'. Zoroastrianism became the state religion during the Sasanian period (third-seventh centuries AD).

The Persian kings adopted a policy of religious tolerance and allowed local religions to flourish throughout the empire. They helped to pay for the building or rebuilding of temples dedicated to foreign gods and religions. The policy was initiated by Cyrus, who returned the Treasures of the Jews and gave official permission for the rebuilding of the Temple of Solomon. It seems that even in the Persian heartland, non-Zoroastrian gods were revered: on the Cyrus Cylinder, for example, Cyrus speaks respectfully of the Babylonian city-god Marduk.

Priests in Iran were called magi, and some of them also held administrative positions at court. They are sometimes shown in the art of the period, performing ritual ceremonies. The ceremony most frequently depicted on the reliefs seems to have been called 'Ian', which appears to have involved offerings of food and drink. It was performed by both Iranians and Elamites, and the inscriptions imply that there was a degree of cooperation between priests of different religions.