Borrowed from Classical Mongolian ᠮᠣᠩᠭᠣᠯ (mongɣol), from Middle Mongol ᠮᠣᠩᠬᠣᠯ (mongqol).
The sense “person with Down syndrome” comes from the fact that people with this condition often have a prominent epicanthic fold, as most people of East Asian ethnicity do.