He will take over team management affairs with immediate effect.
Steve Cotterill regarded in the game as being one of the brightest young coaches joins as number two to Wilkinson.
Wilkinson told the club's official website: "I relish the challenge ahead here at Sunderland.
"It is clear to me that this is a club with a proud tradition, huge and faithful support and in the Stadium of Light and academy, facilities that will be second to none.
" I feel that I have benefited massively from my time as Technical Director at the FA. It was a great opportunity to take a step back from the narrow focus that club management can have and look at the new and modern developments that were occurring in the game. I am very grateful to Adam Crozier and the FA for understanding that the position at Sunderland is challenging and exciting at this stage in my career.
" I am really looking forward to working closely with Steve to develop what is on paper already a strong squad at Sunderland. Steve has established a tremendous reputation within the game in a relatively short space of time. With my experience and Steve's undoubted ability, I see bright and exciting times ahead for Sunderland Football Club and its supporters. "