Wilson, who has been with City for 10 years, will work along manager David Moyes and chief executive Martin Bain from 1 January.
Bain said Wilson will have input into "scouting, recruitment, medical services, player pathways and youth development" in the new role.
He previously worked with Moyes at Preston North End.
"My role will be to ensure that we have the best practices, systems and people in place in order to give the club the best platform to achieve its goals," said Wilson.
Sunderland have appointed Manchester City's director of football services Simon Wilson as chief football officer.