The hosts made a good start with the first two chances falling to Paddy Madden. First, the striker met a cross and volleyed into the ground, which goalkeeper Jackson Smith claimed, before shortly after he blazed wide after finding space in the box.
A counter-attack then saw Elliot Newby almost squeeze the ball in at the far post, but Smith was equal to it.
However, Wolves still carried a threat. A lovely move started with Chem Campbell nutmegging his opponent before the ball was quickly moved to Tyler Roberts, who set up Ollie Tipton from the edge of the box. His powerful effort was spilled by goalkeeper Ben Hinchliffe, but Stockport cleared their lines.
After 20 minutes, Wolves took the lead. A quick counter-attack saw Campbell in space and his shot trickled through to Lee Harkin, who took a composed touch around the goalkeeper and finished into an empty net.
As Stockport looked to get back into the game, Filozofe Mabete made an error by letting the ball bounce in the box, which Madden pounced on. He poked it towards Connor Jennings, who directed his header wide.
Campbell was impressing and almost scored when he met a cross, but his header was saved, before Harkin curled a lovely effort towards the far post and missed the target by inches.
The last major action of the half saw Campbell smash the post with a 25-yard free-kick as Wolves took their one-goal advantage into the break.
The first chance of the second half fell to Stockport, as Smith had to tip Miles Hippolyte’s header over the bar.
The hosts were having the better of the play and Madden had the ball in the net after 58 minutes, but it was rightly chalked off for an obvious foul in the build-up.
Wolves were struggling to create but were handed a gift when Roberts intercepted a poor pass, raced towards goal and tucked the ball into the bottom corner to make it 2-0.
Harkin almost got his second after a swift counter-attack, but the goalkeeper was equal to it, and Hinchliffe was called upon again to turn an effort around the post from Campbell after a sublime solo run.
Jennings scored a late goal for Stockport but Wolves hung on to continue their winning run in the competition. Port Vale’s victory at Shrewsbury mean both Vale and Wolves are guaranteed a place in the knockout stages and their clash next month will determine who tops the group.
Wolves U21: Smith, Lembikisa, Mabete, Kandola, Tipton, Bueno, Griffiths, Hodnett (Matheson, 60), Roberts, Harkin, Campbell.
Subs not used: Storer, Chiwome, Keto-Diyawa, Kaleta, Ojinnaka, Farmer.
Stockport: Hinchliffe, Kitching, Palmer, Evans, Madden, Rydel (Wootton, 66), Newby, Hippolyte, Jennings, Johnson (Croasdale, 66), Lewis (Brown, 22).
Subs not used: Jones, Horsfall, Sarcevic, Barugh.