Pain in a north German city (6)
I believe the answer is:
aachen
'german city' is the definition.
(I've seen this before)
'pain in a north' is the wordplay.
'pain' becomes 'ache' (ache is a kind of pain).
'in' indicates putting letters inside.
'north' becomes 'N' (abbreviation).
'a'+'n'='an'
'ache' going inside 'an' is 'AACHEN'.
(Other definitions for aachen that I've seen before include "German name for Aix-la-Chapelle" , "Aix-la-Chapelle's other name" , "old capital city" , "spa town" , "Whither good news was brought" .)