However, the story won't be published, instead going up for auction to raise money for Waterstone's What's Your Story? charity scheme.
Rowling and 13 other authors - including Nick Hornby, Doris Lessing, Irvine Welsh, Sebastian Faulks and Margaret Atwood - all penned storycards for the book retailer, each of which will go under the hammer at Waterstone's Piccadilly store on June 10.
Managing director of Waterstone's Gerry Johnson said: "What's Your Story just gets more and more exciting. All these brilliant works by amazing writers and illustrators, every one a small masterpiece, and now this - the prequel to Harry Potter.
"We never dreamed that J.K. Rowling would donate something so precious, and we're incredibly grateful."
Money raised from the auction will go to English PEN and Dyslexia Action.
"Given the enormous interest we have seen in recent times for autograph work by J.K. Rowling, the prospects for her storycard are good to say the least," said Philip Errington of Sotheby's.
"There is just no telling how high the bidding might go."