The author will be co-producer on the project and will work with the writer on the new play, but will not script it herself.
The production will "explore the previously untold story of Harry's early years as an orphan and outcast", according to the team behind it.
Rowling, who lives in Scotland, is working with theatre producers Sonia Friedman and Colin Callender on the project, which they will begin to develop in the New Year.
She said: "Over the years I have received countless approaches about turning Harry Potter into a theatrical production, but Sonia and Colin's vision was the only one that really made sense to me, and which had the sensitivity, intensity and intimacy I thought appropriate for bringing Harry's story to the stage. After a year in gestation it is exciting to see this project moving on to the next phase."
No writers or directors have yet been signed for the project. Earlier this year Rowling was unmasked as the writer behind crime novel The Cuckoo's Calling, which she secretly wrote under the pseudonym Robert Galbraith.