A superb second-half fightback saw the Clarets score four times to secure the win which took them up to second spot in the Professional Development League’s northern group.
Trailing 2-0 at the break, Burnley’s three-game unbeaten run was in danger of coming to an end.
But Steve Stone’s youngsters raised their game to dominate the second half at Leyland’s County Ground and complete the double over their Lancashire rivals.
Three days after drawing with Liverpool to enhance their chances of progressing in the Premier League Cup, the Clarets made a handful of changes as midfielder Christian N’Guessan and defender Teddy Perkins both returned from long-term injury.