In the 6th century BC the Achaemenian ruler Cyrus II the Great established his authority over the area. Darius I the Great consolidated Achaemenian rule of the region through the provinces, or satrapies, of Aria (in the region of modern Herat), Bactria (Balkh), Sattagydia (Ghazni to the Indus River), Arachosia (Qandahar), and Drangiana (Seistan).

Alexander the Great overthrew the Achaemenians and conquered most of the Afghan satrapies before he left for India in 327 BC. Ruins of an outpost Greek city founded about 325 BC were discovered at Ay Khanom, at the confluence of the Amu and Kowkcheh rivers. Excavations there produced inscriptions and transcriptions of Delphic precepts written in a script influenced by cursive Greek. Greek decorative elements dominate the architecture, including an immense administrative centre, a theatre, and a gymnasium. A nomadic raid about 130 BC ended the Greek era at Ay Khanom.

After Alexander's death in 323 BC, the eastern satrapies passed to the Seleucid dynasty, which ruled from Babylon. In about 304 BC the territory south of the Hindu Kush was ceded to the Maurya dynasty of northern India. Bilingual rock inscriptions in Greek and Aramaic (the official language of the Achaemenians) found at Qandahar and Laghman (in eastern Afghanistan) date from the reign of Asoka (c. 265-238 BC, or c. 273-232 BC), the Maurya dynasty's most renowned emperor. Diodotus, a local Greco-Bactrian governor, declared the Afghan plain of the Amu River independent about 250 BC; Greco-Bactrian conquerors moved south about 180 BC and established their rule at Kabul and in the Punjab. The Parthians of eastern Iran also broke away from the Seleucids, establishing control over Seistan and Qandahar in the south.