"tiny human being produced artificially," 1650s, from Latin homunculus (plural homunculi), literally "little person," with -culus, diminutive suffix, + homo (genitive hominis), which technically meant "male human," but it also was used with a sense "the human race, mankind;" while in Vulgar Latin it could be used as "one, anyone, they, people" and in logical and scholastic writing as "a human being, person."
This is conjectured to be from PIE *(dh)ghomon- (source also of Old Irish duine, Welsh dyn, Breton den "man;" Old Prussian smunents, smunets "man;" Old Lithuanian žmuo "person," Lithuanian žmogus "man," žmones "people," Gothic guma, Old High German gomo, Old Norse gume, Old English guma "man"). The literal sense is "earthling," from PIE root *dhghem- "earth" (compare human (adj.)). Other Latin diminutives from homo included homullus, homuncio.