Wilkinson steps up from the U18s and replaces Brian Barry-Murphy.
“I’m very excited and very privileged to have taken up the role,” Wilkinson told City's website.
“It’s the pinnacle of Academy football, and effectively the second team in Manchester City so it’s an enormous honour.
“In terms of my approach to the position, I think over the last three or four years we’ve had a relatively successful model which has worked.
“It’s about bridging that gap now going from the Under-18s to Under-21s. What do the players need to get them to first team level and how does that affect my behaviours with them and what they need from me?
“I think fine tuning is probably a good word to describe it.
“We’ve had some good memories in that journey with a lot of them (through the age groups).
“So, hopefully we can fuel off that and try and take it into a successful season for the boys as individuals and then also as a collective group.”