The youth team suffered a 1-0 defeat away to Sheffield United in the Professional Development League.
Harrison Neal’s 58th minute strike proved to be the difference between the two sides.
Michael Fowler started for the Clarets, despite recently joining Padiham on a work experience loan.
The Storks were involved in the FA Vase competition this weekend, leaving Fowler ineligible.
Although assistant manager John Townson admitted it was a tough decision to drop Mitch George to the bench, after netting the winner last weekend.
He explained: “It was a very tough decision, I think to be honest Mike has performed very well in a period of games now, but Mitch got that opportunity last week and took it with Mike going out on loan.
“The bigger picture is that Mike will be out on loan now and involved with Padiham, which will open the door for Mitch again to step in”.
The Clarets started the game brightly and came close early on, as Kai Smith picked up the ball outside the area, before curling an effort inches wide of the post.
Danny Cadamarteri’s side then had another chance shortly after, as Rhys Fenlon cut inside the area and rattled the crossbar.
Fenlon was in action again moments later, as his strike this time fizzed just wide of the post.
However, it was the Blades who struck first. The ball fell to Neal at the edge of the box from a corner and the midfielder rifled home into the bottom corner.
Kian Yari came close to an equaliser, as his effort from 20 yards out sailed just over the bar.
Despite Burnley’s best efforts at clawing one back, the hosts held their line and kept the Clarets at bay to ensure all three points.
However, Townson still felt there were positives to take from the match.
He said: “It is disappointing, especially to come away without a clean-sheet and it’s a set-piece that they scored from.
“It’s a great strike to be fair, but I’m just disappointed the defence didn’t get the clean-sheet that they deserved.
“The back-four did a lot better today than they did last week and in spells we looked good when we got into the front four, however we didn’t secure the ball well enough going forward.
“So, I’m looking forward to next week and we know what we need to work on going forward”
Burnley: Allen, Patterson, Pruti, Taylor, Rain, Fenlon, Smith (George 65), Mupariwa, Yari (Major 82), Conn-Clarke (Kershaw 43), Fowler.
Unused subs: O'Shaugnessy, Chima.