Michael Duff’s U23 Development side surrendered a two-goal lead in their league 3-2 defeat against QPR.
Ali Koiki’s deflected cross put the Clarets ahead, before Rob Harker slotted home the second to put the Clarets in control.
However, three goals in 15 minutes from Rangers in the second half secured all three points for the London side.
The hosts looked lively in the opening stages, asNathan Oduwa found space in the area before firing straight at Adam Legzdins.
Rangers came close again shortly after, as Oduwa teed up Sean Goss on the edge of the area. However, the former Manchester United midfielder’s effort was caught well by Legzdins.
The Clarets’ first real chance came with 20 minutes played. Dan Agyei broke forward towards goal, before seeing his strike tipped wide by Marcin Brzozowksi.
Burnley were then inches away from breaking the deadlock, as Olatunde Bayode crossed to the back post for Harker, whose cushioned header was denied by the feet of Brzozowski.
However, minutes later Duff's side did take the lead, as Koiki’s teasing cross into the area was deflected in off a Rangers defender.
It didn’t take long for the Clarets to double their lead.
Christian N’Guessan drove forward on the counter-attack, before squaring to Harker in the area to slot home.
The visitors could have had a third early on in the second half as former Norwich City defender Sebastian Bassong, who is currently on trial with the R’s, was accused of handling in the area.
Agyei stepped up to take the penalty, however the forward blazed the ball well over from the spot.
Moments after, QPR pulled one back as substitute Deshane Dalling curled the ball into the far corner past Legzdins.
And 10 minutes later, the R’s had their equaliser, as Aramide Oteh headed home at the back post on the 80 minute mark.
The home side then had the momentum and took the lead with five minutes to go, as Ilias Chair smashed home from close range to complete the turnaround
And despite the Clarets’ best efforts at snatching a late equaliser, the home side held on to ensure all three points, to leave Duff disappointed.
He said: "We were excellent for 60 minutes of the match until the penalty and we then dropped too deep and allowed them to come on us.
"From then on we couldn't get up the pitch.
"I'm disappointed with the goals we conceded, especially as it's the second game we have been 2-0 up at half-time and gone on to lose.
"However, there were a couple of positives to take, from midfield duo N'Guessan and Goodridge and also Agyei up top."
BURNLEY: Legzdins, Cropper, Cook, Younger, Koiki, Bayode (Clarke 84), N’Guessan, Goodridge, Blair (Chakwana 57), Harker (Glennon 73), Agyei.
Unused subs; McMahon, Perkins.