Pain in the side, an irritation on the way (6)
I believe the answer is:
stitch
'pain in the side' is the definition.
(I've seen this before)
'an irritation on the way' is the wordplay.
'an irritation' becomes 'itch' (I've seen this before).
'on' means one lot of letters go next to another.
'the way' becomes 'st'.
'itch' after 'st' is 'STITCH'.
(Other definitions for stitch that I've seen before include "A result of running" , "Sew - sharp pain in side" , "Perform final act in theatre" , "Sort of pain" , "Pain caused by running" .)