Joe McGlynn grabbed another goal as the youths secured their first win in the Clarets Cup.
McGlynn (above) followed up his hat-trick in the Clarets’ opening group game in the competition with a fifth goal of the campaign as Tony Philliskirk’s youngsters struck twice after the break to take the points.
Ben Woods put the Clarets ahead from the penalty spot
The sides swapped goals before half-time at the Barnfield Training Centre with Ben Woods scoring from the penalty spot to give the hosts an early lead.
McGlynn, who also netted the winner as Burnley got off the mark in the U18 Professional Development League with victory over Cardiff City last Saturday, ran through to make it 2-1 with a calm finish early in the second half as the Clarets took control.
And with 25 minutes to go, Under-16s’ forward Ruairi Behan capitalised on hesitation in the Owls’ defence to slot home and extend the Clarets’ unbeaten start in Group A following a 4-4 draw with Preston in their opening fixture in the re-vamped tournament.
"I was really impressed with how we came out at the start of the second half and played on the front foot," said assistant boss John Townson.
"It was also pleasing to see how we managed the game in the final 20 minutes.
"After letting a 3-1 lead slip last week it was important we showed we had learned from that and the players took the work we did after that on board."
Burnley: Thomas, Connolly, Trialist (Rooney 86), Carson, Armstrong, Trialist (Eastmond 75), Moonan, Woods (Brennan HT), Trialist, Behan, McGlynn.