late 14c., "to cast down" (a sense now obsolete), from Old French aflicter, from Latin afflictare "to damage, harass, torment," frequentative of affligere (past participle afflictus) "to dash down, overthrow," from ad "to" (see ad-) + fligere (past participle flictus) "to strike," from PIE root *bhlig- "to strike" (source also of Greek phlibein "to press, crush," Czech blizna "scar," Welsh blif "catapult").
The weakened or transferred meaning "to trouble in body or mind, harass, distress," is attested from 1530s. Related: Afflicted; afflicting.