1520s, "lofty with pride, haughtily contemptuous," from Latin superciliosus "haughty, arrogant," from supercilium "haughty demeanor, pride," literally "eyebrow" (via notion of raising the eyebrow to express haughtiness), from super "above" (see super-) + second element akin to cilium "eyelid," related to celare "to cover, hide," from PIE root *kel- (1) "to cover, conceal, save." Related: Superciliously; superciliousness.
Since cilium is more recent than supercilium, the former can be interpreted as a back-formation to the latter .... If indeed derived from the root *kel- 'to hide', we must still assume that a noun *kilium 'eyelid' existed, since the eyelid can 'hide' the eye, whereas the eyebrow does not have such a function. Thus, supercilium may originally have meant 'what is above the cilium'. [Michiel de Vaan, "Etymological Dictionary of Latin and the other Italic Languages," Leiden, 2008]