Burnley started the brighter in this clash, as a set piece routine from the Clarets found skipper Glennon who cannoned his effort against the bar from point blank range.
Minutes after and Wanderers were ahead, after Stephen Duke-McKenna played the ball to Ronan Darcy, who delayed his pass into Oluwale Tanimowo just enough for the striker to calmly place his effort into the bottom right corner.
Darcy nearly provided another assist moments later, as a cross field ball to Wanderers skipper Harry Brockbank saw the full back fire towards Burnley's goal from some distance, forcing a smart save from Aiden Stone.
Burnley responded just after the half hour mark, with Rob Harker creating space on the edge of the penalty area to create a strike on goal but his effort curled wide of the goal.
With six minutes to go in the first period, Tanimowo made it two for David Lee's men.
Shakeel Jones-Griffiths did excellenty well to close down a Clarets defender, before playing in the striker, who placed the ball into the bottom corner leaving Stone helpless to stop it finding the net.
After the restart, Burnley came out with a spring in their step.
A minute prior to the hour mark and the visitors got one back, as a goal line scramble from a corner saw Michael Fowler back heel the ball into the bath of the net.
Three minutes after and Burnley had levelled proceedings, as another set play from Steve Stone's men saw Bobby Thomas latch onto a near post ball into the area by Josh Benson to stick it past Jake Turner.
Burnley began to step it up a notch, with their new found confidence under their belts.
Fowler should have put the Clarets ahead with 13 minutes to go, as he was left unmarked in the area but a header lacking power fell into Turner's hands.
But soon after, the visiting side took the lead as a free kick into the area saw second half substitute Dan Agyei lose his man and power his header past Turner into the bottom right corner.
Three soon became four, as Benson curved a free kick around Bolton's wall and into the top corner to seal all three points for the visitors in this Professional Development League clash.
Wanderers XI: Turner, Brockbank (C), Johnson, Zouma, Hartshorne, Earing, Doyle, Jones-Griffiths, Tanimowo, Duke-McKenna, Darcy.
Substitutes: White, Aspinall, Boon, Navarro, Brown.