Idiot in school's a pain (6)
I believe the answer is:
stitch
'a pain' is the definition.
(pain in the body)
'idiot in school's' is the wordplay.
'idiot' becomes 'tit' (both can mean a stupid person).
'in' means one lot of letters goes inside another.
'school' becomes 'sch' (abbreviation).
'tit' placed inside 'sch' is 'STITCH'.
(Other definitions for stitch that I've seen before include "Something surgeon provides" , "Link, loop or knot made in knitting or sewing" , "A sewer may produce such" , "something seen in the needlework class" , "One in time is said to save nine" .)