In their first match since winning the Final Third Development trophy last month, a young Clarets side led through a trialist, before the Latics came storming back to clinch victory.
It was Michael Jolley's side that got the ball rolling early on, as Jamie Thomas – currently enjoying a loan spell with Ayr United - played in youngster Ali Koki, who squared the ball into the box for Robbie Leitch to fizz a shot just wide.
However, Burnley's attacking play paid off as the trialist chased the ball and latched onto Sam Stubbs' mistake and slotted neatly past Dan Lavercombe in the Wigan goal.
It didn't take long for the Latics’ to reply though, as Stubbs redeemed himself for the earlier mistake and nodded home a header from a corner to pull the score level just 15 minutes in.
The Clarets responded and Mark Howarth whipped in a delightful ball to the back post which found skipper Jimmy Dunne. However, the former Manchester United defender saw his header fly wide.
Wigan we're not holding back either and Josh Gregory put the visitors 2-1 up just before the break as he curled a shot into the far corner outside the box past a stranded Tony Aghayere in the Burnley goal.
The away side were inches away from going 3-1 up early on in the second half, as Gregory tried an effort 25 yards out that skimmed past the post.
And as the ebb and flow continued, the Clarets came close to equalising just past the hour mark as the trialist came close again, following Brad Jackson’s pass.
And despite the hosts’ best effort to get a second half equaliser, the Latics sealed the win when Sam Cosgrove doubled the advantage in the 75 minute.
BURNLEY: Aghayere, Birch, Olomowewe (Mpofu 72), Dunne, Koki, Leitch (Bayode 55), Howarth (Trialist 55) Yao, Jackson, Thomas (Trialist 60), Trialist.