The 17-year-old was on the Bulls' books last term and last night tweeted that he had agreed a three-year deal to sign for City.
All of Stephen Clemence's development squad will be based at Bishop Burton this season, an under-21s side which they are trying to further strengthen ahead of the new season.
City had been closing in on a move for Bristol Rovers rookie Alefe Santos, who turned down a contract offer from Bristol Rovers this month.
A transfer fee would have been set by a tribunal but the 19-year-old today opted for a move to Derby County ahead of the KC Stadium.
Bowen's move into City's development ranks underlines the club's desire to strengthen options beneath the first team fold.
A much-improved under-21s group is being sought over the next two seasons as the signing of Johan Ter Horst, a £30,000 signing from Folkestone Invicta, and Calaum Jahraldo-Martin, who joined the club in a similar deal from Dulwich Hamlet 15 months ago shows.
