Rowling, who recently donated £10 million to set up a new multiple sclerosis research clinic in Edinburgh, was chosen for her writing skills, tenacity to succeed and philanthropic nature, the National Magazine Company said.
Pop star turned fashion designer Victoria Beckham was the runner-up with the Queen in third place. The prime minister's wife Samantha Cameron was sixth.
The list of 100 women was compiled to mark the centenary of the National Magazine Company which currently publishes 20 magazines.
In a separate list, business magazine Forbes last week named Michelle Obama as the world's most powerful woman with the Queen, the only British national to feature in the top 100, placed 41st.
