Teenagers Chris Conn-Clarke and Max Thompson both scored their first goals for the Under-23s as the Clarets bounced back in style to go back to second place in the league table.
A youthful Burnley side had lost three of their last four games in a transitional period which has seen many of the squad’s more senior players head out on loan.
Seven scholars therefore lined up at Leyland’s County Ground as the Clarets - missing Ollie Younger, Ali Koiki and Bobby Thomas through a combination of injury and illness - fielded their youngest line-up of the season.
But they rose impressively to the challenge to comfortably beat the bottom club in the Professional Development League’s northern group with classy finishes in either half to go back above Leeds United – who had drawn earlier in the day – and three points behind table-topping Nottingham Forest.
The Clarets were outstanding before the break and deserved more than the one-goal lead given them in the final minute of the first half by Conn-Clarke.
The Northern Irishman, and Ne-Jai Tucker on the opposite flank, caused constant problems for the Bolton back line and both could have scored before Conn-Clarke finally found a way through.
Tucker first teed up Conn-Clarke for a shot Matthew Alexander did well to keep out.
And Conn-Clarke then returned the favour for his opposite wingman to lift a shot over the top when he should have hit the target from 10 yards out.
Tucker also sent another effort just over the bar as he drifted in from the right flank to great effect, while Thompson also carried a threat on his first start at this level.
Bolton had won only one previous game and were thumped 5-0 in the return fixture in December.
But they boasted some experience in their ranks in the shape of new signings Jacob Mellis and Ryan Delaney and former Rochdale man Joe Bunney.
And it was centre-back Delaney who went closest for the home side when he saw a volley blocked in front of goal following a corner.
The Clarets always looked the most likely scorers, though, and finally got their reward with an excellent goal in the 45th-minute.
Mace Goodridge, providing a solid midfield platform alongside first-year scholar Ben Woods, sparked the move with a ball wide to Matty Rain.
The full-back then released Conn-Clarke, who cut into curl a trademark right-footer beyond Alexander and into the far corner.
In driving wind and occasional rain, the second half was a more scrappy affair.
But Andy Farrell’s side were always in control and again created the better opportunities.
Thompson saw an angled strike saved by Alexander after he had been released by Joel Senior’s fine pass, while substitute Mitch George saw a shot blocked in front of goal.
The introduction of George, Kane Patterson and Rhys Fenlon took the number of scholars on duty to 10.
And all were helped along by skipper Jimmy Dunne, a tower of strength at the back alongside debutant Edon Pruti.
Dunne just avoided putting the ball into his own net when he did well to cut out a low cross in the nearest Bolton came to an equaliser.
But with six minutes to go the Clarets wrapped up a tenth and one of the most satisfying wins of the campaign through Thompson.
Fenlon showed his pace and eye for a pass to release the striker – who continues to look a decent acquisition following his release from Everton – and the 17-year-old did the rest with clinical finished, steered into the bottom corner from just outside the penalty area.
Bolton: Alexander; White, Edwards, Delaney, Senior (Ahmadi 60); Darcy Mellis, Thomason, Bunney; Faal, Graham. Substitutes: King-Harmes, Hutchinson, Brown-Sterling, Richards.
Burnley: Jensen; Senior (Patterson 75), Dunne, Pruti, Rain; Tucker, Woods, Goodridge, Conn-Clarke (Fenlon 75); Thompson, McGlynn (George 62). Substitutes: McMahon, Rooney.
Referee: Richard Holmes