early 14c., ruffelen, "to disturb the smoothness or order of," a word of obscure origin. Similar forms are found in Scandinavian (such as Old Norse hrufla "to scratch") and Low German (ruffelen "to wrinkle, curl;" Middle Low German ruffen "to fornicate"), but the exact relation and origin of them is uncertain. Also compare Middle English ruffelen "be at odds with, quarrel, dispute."
The meaning "disarrange" (hair or feathers) is recorded from late 15c.; the sense of "annoy, vex, distract" is from 1650s. Related: Ruffled; ruffling.
"ornamental frill of textile material drawn up at one end in gathers or plaits," 1707, from ruffle (v.). The sense of "disturbance, perturbation" is by 1704.