Pain in mouth cut windpipe (7)
I believe the answer is:
trachea
'windpipe' is the definition.
('trachea' can be a synonym of 'windpipe')
'pain in mouth cut' is the wordplay.
'pain' becomes 'ache' (ache is a kind of pain**).
'in' means one lot of letters goes inside another.
'mouth' becomes 'trap' (informal term for mouth).
'cut' means to remove the last letter.
'trap' with its final letter removed is 'tra'.
'ache' put within 'tra' is 'TRACHEA'.
(Other definitions for trachea that I've seen before include "get air supply through this" , "airy passage" , "Tube taking inhaled air from the larynx" , "airway" , "where air passes" .)