An early goal from Alex Whitmore was enough to give the Clarets' Development Squad a second successive 1-0 win.
Whitmore, back from a loan spell at Morecambe, scored after just three minutes as Michael Jolley's side followed up last week's win over Fleetwood with a similar victory at Christopher Park.
The decisive moment came after the Clarets forced a corner when Aiden O'Neill's effort was saved by Wigan keeper Owen Evans.
The delivery fell to Whitmore (above) at the far post for the defender to slot home what proved to be the winner.
Burnley came close again as birthday-boy Jamie Thomas broke through on goal, one-on-one with Evans, before firing just wide.
Wigan then had their first opportunity of the game when midfielder James Boyd tested Conor Mitchell from distance but the Northern Ireland under-21 international was up to the task.
O'Neil then tested Wigan keeper Evans again as his driving effort from 25 yards out was parried out before the keeper held the ball at the second attempt.
Sam Cosgrove then came close to handing the home side an equaliser when his shot from just inside the area was superbly tipped onto the under-side of the cross bar by Mitchell.
The recent return of Dan Agyei and Ntumba Massanka from their loan spells at Coventry City and Morecambe respectively saw the pair start up top together.
And the duo combined well in the second half as Burnley almost doubled their lead.
After linking up well, Massanka played in Agyei who weaved in and around the area before Latics' defender Liam Langford made a vital block to clear the danger.
Burnley: Mitchell, Birch, Dunne, Whitmore, Koiki, Jackson (Olomewewe 61) , O'Neil, Trialist, Thomas (Leitch 56) , Ageyi, Massanka. Subs not used: King.