Fool leaves class in thought, probably having done a lot of working out (7)
I believe the answer is:
Here is my best explanation:
'probably having done a lot of working out' is the definition.
I can't tell whether this definition defines the answer.
'fool leaves class in thought' is the wordplay.
'fool leaves class' becomes 'cl' (I am not sure about this - if you are sure you should believe this answer much more).
'in' means one lot of letters goes inside another.
'thought' becomes 'mused' (musing is a kind of thinking).
'cl' inserted into 'mused' is 'MUSCLED'.
(Another definition for muscled that I've seen is "brawn?".)