Jolly Roger’s head case (5)
I believe the answer is:
skull
'head case' is the definition.
'skull' can be an answer for 'head' (I've seen this before). I'm not certain of the 'case' bit.
I cannot understand how the remainder of the clue works.
Can you help me to learn more?
(Other definitions for skull that I've seen before include "Pirate flag feature" , "Bony part of head" , "Bony skeleton of the head" , "Head structure" , "Bony frame of head ..." .)