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1520s, 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- "to conceal" (see cell).
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]