Old English run, rune "secret, mystery, dark mysterious statement, (secret) council," also "a runic letter" (runstæf), from Proto-Germanic *runo (source also of Old Norse run "a secret, magic sign, runic character," Old High German runa "a secret conversation, whisper," Gothic runa), from PIE *ru-no-, source of technical terms of magic in Germanic and Celtic (source also of Gaelic run "a secret, mystery, craft, deceit, purpose, intention, desire," Welsh rhin "a secret, charm, virtue"). Also see Runnymede.
The word entered Middle English as roun and by normal evolution would have become Modern English *rown, but it died out mid-15c. when the use of runes did. The modern usage is from late 17c., from German philologists who had reintroduced the word in their writings from a Scandinavian source (such as Danish rune, from Old Norse run). The runic alphabet is believed to have developed by 2c. C.E. from contact with Greek writing, with the letters modified to be more easily cut into wood or stone.