Pair, say, up in pain (6)
I believe the answer is:
twinge
'pain' is the definition.
(twinge is a kind of pain)
'pair say up' is the wordplay.
'pair' becomes 'twin' ('twin' can be a synonym of 'pair'**).
'say' becomes 'eg'.
'up' is a reversal indicator (in down clue: letters go upwards).
'eg' back-to-front is 'ge'.
'twin'+'ge'='TWINGE'
'in' is the link.
(Other definitions for twinge that I've seen before include "Brief sharp pain" , "Brief sudden pain" , "Spasm" , "Sharp pang" , "Sudden stab of pain" .)