Peter Beardsley and Ben Dawson's young side will be playing in the revamped competition for the first time this term, and have been drawn in Group D in the Northern section.
They will face two League Two sides in Crewe and Port Vale, while they will also come up against League One opposition in the shape of John Sheridan's Latics.
Each team will play each other just once in the group stage, with the 16 invited academy sides - including the Magpies - set to play one of their fixtures at home.
In order to progress to the round of 32, United must finish in first or second place in their group.