Danny Cadermarteri's youth team ended Millwall's winning start to the season as Michael Fowler made it three goals in three games to secure a first home win of the campaign for the Clarets.
Burnley got off to a great start as they looked to follow up their opening win in the Professional Development League a week ago at Cardiff against a Millwall side which had won its opening two matches.
And the Clarets came close to an early goal when Dwight McNeil's in-swinging free-kick was met by James Clarke at the far post for the skipper to head against the crossbar before Millwall keeper Sam Jackson cleared the danger.
The Clarets then had a glorious chance when Fowler took advantage of a poor goal-kick before rounding Jackson and firing just wide.
However, minutes later the home side did take the lead when McNeil curled in a fine free-kick which found Dan Moss in the area.
Moss pulled off an extraordinary bicycle kick, forcing Jackson into a smart save, but Fowler (abwas there to tap home the winner and make it three goals in as many games for the first-year striker.
Millwall went in search of an equaliser early in the second half when Jesse Debrah's towering header looped just over Adam Bruce's bar.
The Lions then tested Bruce as Bessart Toppaloj sparked a dazzling run from the back, all the way into the area before rifling an effort straight at the Burnley keeper.
Cadermarteri's side came close to doubling the lead as Dylan Meredith beat Junior Tiensia before whipping a ball for McNeil who lurking at the far post.
The winger put his header just wide of Jackson's goal but the Clarets had done enough to secure the points and make it an impressive start to life in new surroundings.
Burnley: Bruce, Clarke, Younger, Wilson, Mpofu, Meredith (Egan 83), Kershaw, Yari, Moss, McNeil, Fowler. Subs: Wusiewicz, Taylor, Harris, Thomas.