Kwesi Donsu's super goal in the second half ensured Medeama ended WAFA's unbeaten 46 home match run to win 2-1 in Sogakope on Wednesday.
But it was the Academy Boys who scored first through Charles Boateng-making his first start since recovering from an operation-in the 24th minute.
Left back Francis Boateng sent in a cross which was flicked on by Aminu Mohammed to the far which where Boateng, unmarked, connected home from close range.
Against the run of play, Medeama were level before the half time whistle.
Defender Justice Blay applied a header to a corner kick from their attacking right wing and it went through the hands of of goalkeeper Richmond Ayi.
In the 57th minute, Donsu scored a worldie when his powerful volley from the right-close to the corner flag-zoomed into the net at the far side like a missile.
WAFA tried to stage a comeback and salvage a point but the youngsters lacked the firepower.
It has been three straight defeats after the 2-0 and 1-0 reverses to Elmina Sharks and Inter Allies.