The 19-year-old, who has enjoyed a breakthrough season at Old Trafford, is widely regarded as one of the best young talents in European football.
He had been eligible to represent Belgium through his birth and passport, Albania through his heritage, Turkey through his grandparents, as well as Serbia and Kosovo.
It had been claimed on a number of occasions that the teenager would choose Albania after refusing a call-up to the Belgium squad last year.
However, on his official Twitter account, Wilmots has said that Januzaj has now chosen to represent the country of his birth.
England were also believed to be monitoring proceedings.