Pupils get 99 in Latin - great work! (7)
I believe the answer is:
classic
'great work' is the definition.
(eg a literary classic)
'pupils get 99' is the wordplay.
'pupils' becomes 'class' (I've seen this before).
'get' says to put letters next to each other.
'99' becomes 'IC' (Roman numerals).
'class'+'ic'='CLASSIC'
'in latin' acts as a link.
This may not be right. Some or all of it may belong to another bit of the clue.
Can you help me to learn more?
(Other definitions for classic that I've seen before include "The Derby or The Oaks, for example" , "Important horse race" , "Very great work of art" , "Creation of the highest standard" , "Accepted as excellent" .)