She hopes the clinic, to be based at the University of Edinburgh, will become a world centre for excellence in its field.
The facility will also aim to help researchers find out more about other incurable neurological conditions, such as Alzheimer's disease, Parkinson's disease and motor neurone disease.
The clinic will be named after Rowling's mother Anne, who suffered from MS and died at the age of 45.
The author said the new clinic, which is expected to be completed within a year, will place patients at the heart of the research and treatment process.
Rowling said in a statement: "It is with great pleasure and pride that I am donating 10 million pounds to the Regenerative Neurology Clinic at the University of Edinburgh, which is to be named after my mother, Anne.""I am incredibly impressed by the calibre of clinicians and researchers that Edinburgh has already managed to attract to make this project a reality, and I truly believe that it is set to become a world centre for excellence in the field of regenerative neurology."
The Anne Rowling Regenerative Neurology Clinic will be based in a purpose-built facility within the University's Chancellor's Building, next to the city's Royal Infirmary at Little France.
It follows the setting up of the Centre for Multiple Sclerosis Research at the university three years ago, which also received support from the author.
The university said Rowling's 10 million pounds is the single largest donation she has given to a charitable cause. It is also the largest single donation the University has received.