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The name Zagros is derived from the Zagarthians/Sagarthians--and Indo-European, Iranic immigrants from Europe who once inhabited the mountains, from the shores of Lake Van to the coasts of Makran. The Zangana and Chigini tribes of the Kurds are the remnants of these ancient Sagarthians.
Other explanations deriving the name from Greek Zagreus, meaning stormy, or the name Za-G'R' means 'great mountain' in the Avestan language, are invalid.
Signs of early agriculture date back as far as 9000 BCE to the foothills of the Zagros Mountains, in cities later named Anshan and Susa. Jarmo is one archaeological site in this area. Shanidar, where the ancient skeletal remains of Neanderthals have been found, is another.

Some of the earliest evidence of production has been discovered in the Zagros Mountains; both the settlements of Hajji Firuz and Godin Tepe have given evidence of wine storage dating between 3500 and 5400 BC.

During early ancient times, the Zagros was the home of "barbarian" peoples such as the Kassites, Guti, and Mitanni, who periodically invaded the Sumerian and/or Akkadian cities of Mesopotamia. The mountains create a geographic barrier between the flatlands of Mesopotamia which is in Iraq and the Iranian plateau.