Tony Philliskirk's U18 side fell to their first defeat in two months with a 2-1 defeat at home to Sheffield Wednesday.
Wednesday took the lead at the Barnfield Training Centre, before Ben Woods equalised for the Clarets.
But the visitors snatched the winner with five minutes to go from the spot.
Burnley started bright and came close when Chris Conn-Clarke fired an effort just over.
However, Wednesday then took the lead from a free-kick, as the towering Owls defender rose highest to crash a header past Lewis Thomas.
Despite the hosts trailing at the break, Philliskirk's side came out raring to go and got their reward.
Midfielder Ben Woods' corner finding the back of the net, to pull the scores level just four minutes into the second half.
Both sides had several chances to take the lead as the clock ticked on, on a crisp morning in Padiham.
With Mitch George coming closest for Burnley, after just mistiming his connection to Fenlon's cross into the area.
But it was Wednesday who struck again, after defender Edon Pruti handled the ball on the line to deny a clear goal, the former Stevenage man was shown a straight red card and awarded a penalty to the away side.
The Owls' skipper stepped up and slammed the ball in from the spot, ensuring all three points went back over the Pennines, in Burnley's first defeat since September 12th.
BURNLEY: Thomas, Patterson, Rooney, Pruti, Rain, Fenlon, Woods, Moonan, Conn-Clarke, Major, George.
Subs: Waller, Armstrong, Chima, McGlynn, Unwin.