City broke the deadlock at Carrington on the stroke of half time through Farid Alfa-Ruprecht, but United drew level 10 minutes into the second-half through Ethan Williams.
However, Jaden Heskey restored City’s advantage on 68 minutes before Will Dickson fired home 13 minutes from time to seal the win and secure the Manchester bragging rights.
Following on from a 4-2 defeat to Inter Milan in the UEFA Youth League in midweek, the City EDS boss was delighted to see his side quickly return to form in Premier League 2.
“From a result perspective we’re really pleased to get three points in what’s always a really tough fixture,” Wilkinson said after the clash.
“Especially off the back of Inter Milan, it’s a really pleasing way to end the week in terms of a result.
“The way the game unfolded, it is a good confidence boost for us knowing that we can suffer in games and still regroup and find a way to win the game.”
Three points against our Manchester rivals means it’s three successive victories for the EDS in Premier League 2 after defeat against Liverpool in our opening league fixture.
And Wilkinson believes that his players are in a prime position to kick on and continue our fine form into the season.
“Now we’re in a position where the team are fit and they’re in a much better place physically which allows us to perform better,” he added.
“It’s a case of us doing the work daily and I’m really confident that as this season goes on, we will get much better as a team. That’s something that I’ve got a lot of confidence in.
“To have some of these big games early in the season and to get over the line as well helps to give the group the confidence as well and just instil that bit of belief that we need and hopefully we can keep growing.”
