Hughes signed the teenager after a short trial spell at the club.
ESPN reports that Stoke have confirmed that the deal for the 15-year-old has been completed.
Damien Francis, a representative of Ngoy's agency said: "He's started well, so we're just going to see how he progresses and gets on.
"In Belgium, he plays for the national team so we've got high hopes for him. For a 15-year-old he's very talented. If he keeps his feet on the ground and works hard, the sky's the limit for him.
"He's a young lad, so he's got to keep his feet on the ground, and work hard in order to make it. He's done nothing in the game, in reality, because he's got a long career ahead of him."