The year 539 BC was a year of the pre-Julian Roman calendar. In the Roman Empire, it was known as year 215 Ab urbe condita. The denomination 539 BC for this year has been used since the early-medieval period, when the Anno Domini calendar era became the prevalent method in Europe for naming years.

• September 25–28? – Battle of Opis: Troops of the Persian Achaemenid Empire under Cyrus the Great decisively defeat those of the Neo-Babylonian Empire.
• October 29 – Fall of Babylon: Achaemenid troops under Gobryas enter Babylon unopposed. Cyrus enters the city, incorporating the Neo-Babylonian Empire into the Achaemenid Empire and turning the latter into the largest in the history of the world up until that point.

• Nabonidus, last king of Babylon
• Belshazzar, co-regent of Babylon