Swansea City Stoke Under-21s Premier League U21s
The Swans striker opened the scoring ten minutes into the first-half after he fired home from a corner.
McBurnie, who joined the Swans from Bradford City in the summer, doubled the lead a minute after the restart as he latched onto a ball from Daniel James to turn his man before slotting past the keeper.
The striker could have sealed his hat-trick had it not been for the acrobatics of Stoke keeper Dale Eve, who also saved well from Josh Sheehan's rifled effort midway through the second-half.
But the young Swans had done enough to pick up a deserved second league win.
The hosts continued to attack, with midfielder Henry Jones firing just wide from the edge of the area moments later.
Stoke pushed for an equaliser but striker Dominic Telford's shot was well saved by Josh Vickers in the Swans goal with 18 minutes on the clock.
Moments later the Swans could have doubled their lead as a ball over the Stoke defence from Liam Shephard put Henry Jones in one-on-one with keeper Dale Eve, but the midfielders' shot flew just over the bar.
The home side continued to probe, and they went within inches of extending their advantage as Ryan Hedges' corner was cleared off the line by the Stoke defence.
The Potters squandered chances for an equaliser before the break as midfelder Ollie Shenton shot just over the bar before Vickers saved low from Telford.
Daniel James found McBurnie, and the striker turned his defender inside the area before slotting past Eve.
The hosts continued to push and could have had a third goal soon after as Stephen Kingsley beat his man to fire a shot on goal but Stoke's keeper Eve palmed the effort over the bar.
Despite their advantage, the young Swans continued to push for another goal and Henry Jones saw his shot deflected for a corner before McBurnie was denied a hat-trick as the Stoke defence clambered his effort off the line.
Stoke then changed formation to give themselves more options up front, and with a two-man forward line they soon saw Telford go close with an effort that rose just over the crossbar.
At the other end, McBurnie's header was acrobatically saved by Eve just past the hour before Stoke created their best chance through defender Johnville Pringle, who raced into the area before seeing his shot blocked.
And the final real action of the game came with 15 minutes to play as Sheehan found space at the edge of the area but his powerful shot was kept out by Eve.