'non-' originates from Latin, specifically the word 'non', where 'non' meant 'not'; 'cranial' originates from Greek, specifically the word 'kranion', where 'kranion' meant 'skull'.

'noncranial' was formed in modern English by prefixing the negative 'non-' to 'cranial'; 'cranial' entered English via Latin 'cranium' from Greek 'kranion', and the combined form came into use in technical/medical contexts.

Initially, the elements meant 'not' and 'skull' respectively, so the compound originally meant 'not of the skull' and this core sense has been retained in its current meaning 'not relating to the skull'.