Joe Hodge put the hosts ahead in the opening stages, only for Kian Breckin to draw us level six minutes later.
Adedire Mebude gave us the lead before half-time before doubling his tally after the break, securing us the three points and seeing us climb to the top of the table.
It wasn't an ideal start for Brian Barry-Murphy's side in the midlands, as we found ourselves behind after just 11 minutes when Hodge turned home Tyler Robert's assist to give the home side the lead.
However, we responded just six minutes later, when Breckin's shot was smothered out by the Wolves defence, only for the ball to fall to Mebude who squared it back for the midfielder to fire home.
Then, with 25 minutes gone, we completed the turnaround as Joshua Wilson-Esbrand found Mebude. The winger fired at goal and with the aid of a deflection off Will Dickson, saw the ball go beyond the Wolves keeper Andreas Sondergaard and send us into the lead.
The City defence were called upon as Wolves were able to create chances in the latter stages of the opening half, but we were able to hold out to ensure we carried our advantage into the break.
At the break, Barry-Murphy brought on Carlos Borges and the winger made an immediate impact, squaring the ball to Mebude to smash home and give us some much-needed breathing space.
And that is how the game finished as despite the home side having more of the chances, we held firm to secure a vital three points on the road.
HOW WE LINED UP
Manchester City Elite Development Squad
Starting XI | van Sas, Carrington, Burns, Taylor, Wilson-Esbrand, Charles, Mebude, Breckin, Dickson, Adam, Bobb.
Substitutes | Borges, Murray-Jones, Knight, Smith, Ogwuru.
Wolverhampton Wanderers U21
Starting XI | Sondergaard, Lembikisa, Bueno, Mosquera, Tipton, Griffiths, Roberts, Hodge, Fraser, Ronan, Campbell
Substitutes | Birtwhistle, Pond, Scicluna, Harkin, Matheson
WHAT IT MEANS
The victory sees us climb to the top of the Premier League 2 table.
We go level on points with Crystal Palace, but our superior goal difference means we sit top with seven games played.
Next up for the EDS is a home clash against Blackburn Rovers.
Kick-off at the Academy Stadium will be at 13:00 on Saturday 8 October.