The Owls Under-21s were beaten 4-1 by Burnley at Bracken Moor on Monday afternoon.
Mackenzie Maltby opened the scoring for Wednesday but the hosts went 2-1 behind after strikes from Michael Mellon and Ne-Jai Tucker.
The Owls could count themselves unlucky to be behind at half time but two second half goals through Joe Westley and Dara Costelloe meant Burnley took three points back to Lancashire.
There was concern late on for Owls substitute Luke Cook who left the field on a stretcher after he appeared to turn awkwardly on his planted foot on the right flank, with manager Neil Thompson later confirming the youngster will be assessed in hospital.
Wednesday got off to a flyer and opened the scoring before the five-minute mark.
Leojo Davidson whipped in a corner straight onto the head of Maltby and the defender nodded home.
The visitors looked certain to equalise 15 minutes in when Costelloe squared across goal to Marcel Lewis, but Jay Glover showed excellent work rate to get back and slide the ball away from the former Chelsea man.
But the Clarets did restore parity moments later, Mellon was sent through one on one with Luke Jackson and the forward calmly slotted past the Owls shot-stopper.
Wednesday would have retaken the lead were it not for Dan Sassi, the defender arrived just in time to clear after Bailey Cadamarteri robbed goalkeeper Sam Waller of possession in the box.
The end-to-end clash continued with both sides showing a determination to attack, but it was the Clarets who took the lead. Tucker found space on the edge of the box and drilled the ball low into Jackson’s far corner.
An entertaining first half came to a close but not before two quickfire chances for Wednesday.
First, Davidson’s sweet bending strike beat Waller but bounced off the crossbar before Paulo Aguas hit a volley just wide of the far post.
The second half was a scrappier affair with little action before Burnley added to their tally on 75 minutes, Westley driving into the box before hitting a low shot inside the front post.
And moments later Costelloe added a fourth. The striker weaved his way through the Owls defence and finished clinically into the bottom corner.
The injury to Cook brought the game to a standstill for several minutes before the referee blew for full time.
A disappointing result for Wednesday but their main concern will be for the young forward’s welfare.
Wednesday: Jackson, Fusire, Aguas, Maltby, Adetoro (Sesay 60), Agbontohoma, Trialist (Shipston 68), Glover, Cadamarteri, Davidson (Cook 68, Phuthi 82), Trueman