1670s, "one who believes in the coming of the (Christian) millennium" (by 1550s in Latin plural form millenarii), from Latin millenarius "containing a thousand," from millenia "a thousand each," from mille "thousand" (see million). With -ian. As an adjective, "pertaining to the (Christian) millennium," from 1630s.
The apparent inconsistency in spelling (-n-, -nn-) results from the fact that millenarian, like millenary, does not contain the stem of the Latin annus year, which is present in millennium .... [Fowler]