The author lived there between the ages of nine and 18 and in 2011 bought the cottage through a property company in her married name.
She paid about £400,000 for the house, which is said to have inspired key elements of the young wizard's story.
Land Registry records show in September 2011, Edinburgh-based Caernarfon Lettings Ltd, which lists the author's husband Neil Murray as a director, bought Church Cottage.
The property was sold by BBC producer Julian Mercer, who himself had bought it off the Rowling family in 1995.