Puzzle when bird is restricted by farmyard disease (6)
I believe the answer is:
bemuse
'puzzle' is the definition.
(I've seen this before)
'bird is restricted by farmyard disease' is the wordplay.
'bird' becomes 'emu' (emu is a kind of bird).
'is restricted by' indicates putting letters inside (I've seen this in other clues).
'farmyard disease' becomes 'bse' (bovine spongiform encephalopathy).
'emu' put within 'bse' is 'BEMUSE'.
'when' acts as a link.
(Other definitions for bemuse that I've seen before include "Confuse, bewilder" , "Confound" , "Cause puzzlement" , "Muddle or stupefy" , "Stupefy, puzzle" .)