1520s (trans.), from Latin evacuatus, past participle of evacuare "to empty, make void, nullify," used by Pliny in reference to the bowels, used figuratively in Late Latin for "clear out;" from assimilated form of ex- "out" (see ex-) + vacuus "empty," from PIE *wak-, extended form of root *eue- "to leave, abandon, give out."
Earliest sense in English is medical. Military use is by 1710. Meaning "remove inhabitants to safer ground" is from 1934. Intransitive sense is from 1630s; of civilian persons by 1900. Replaced Middle English evacuen "draw off or expel (humors) from the body" (c. 1400). Related: Evacuated; evacuating.