The young Clarets suffered their first defeat in four matches, after falling to a 3-2 defeat against Crewe at the Barnfield Training Centre.
Despite taking the lead twice in the game through U16 duo Michael Mellon and Sean Etaluku, the Alex's 83rd minute goal, meant the three points were gifted to the visitors.
It was a wet and windy morning in Lancashire, as five U16s lined up for Tony Philliskirk's side, along with five first-year scholars and just one second-year, in goalkeeper Harry Allen.
Burnley started bright, as Corey Brennan slipped in Mellon with a lovely weighted through ball, which the young striker latched onto, before firing it through the Alex's goalkeeper's legs to give the home side the lead.
But just over 10 minutes later, Crewe equalised through a swift counter attack.
With the sides level at the break, it was Philliskirk's side that came out the better side early in the second half.
Mellon broke down the right and after some excellent footwork and work rate, the forward teed up Etaluku. who fired home from just inside the box, to regain the Clarets' lead.
However, the Alex, who were working their way back into the game, got their equaliser eight minutes later, after a set-piece into the area found it's way over the line, following a goalmouth scramble.
And despite coming close through strikes from Mellon and Jackson, Crewe went on to snatch a late winner, as the rain began to drench the Barnfield Training Centre.
BURNLEY: Allen, Connolly, Rooney, Carson, Armstrong, Behan, Brennan, Jackson, Etaluku, Mellon, Ratchford.
Subs: Thomas, Chima, Walters, Knowles, Hugill.