The prodigious talent, who was recently in the news for receiving prayer from Prophet TB Joshua, was joint-leading scorer for Kieran McKenna's vibrant Academy side. With 12 goals in 19 starts, he was at the hub of most of the Reds' attacking play, racking up a number of assists as well.
The London-born prospect got over 77 per cent of the votes cast on ManUtd site.
He finished ahead of fellow nominees Callum Whelan and Lee O'Connor.
After being presented with the award at Thursday's ceremony at Old Trafford, Gomes told MUTV: " It's a dream come true. Being at a young age, it's things like this you wish for. All the hard work you put in at the training ground - this is the end result.
Angel Gomes is the first 16-year-old to land the prize in its 27-year history.
Gomes had testified publicly in the church that the pains in his ankle and groin had left following his encounter with Prophet TB Joshua, who prayed for him.