Idiot in school becoming a pain (6)
I believe the answer is:
stitch
'a pain' is the definition.
(pain in the body)
'idiot in school' is the wordplay.
'idiot' becomes 'tit' (both can mean a stupid person).
'in' indicates putting letters inside.
'school' becomes 'sch' (abbreviation).
'tit' put inside 'sch' is 'STITCH'.
'becoming' is the link.
(Other definitions for stitch that I've seen before include "A sewer may produce such" , "result of working with needle?" , "Interlinking loop of yarn" , "One in time is said to save nine" , "Sew with thread" .)