"If you were all nine years old I'd feel so much more comfortable," she said.
Edinburgh-based JK Rowling beat off five other contenders, including horror writer Stephen King, Discworld novelist Terry Pratchett and Inspector Morse creator Colin Dexter at the 11th annual British Book Awards.
The judges, who were drawn from the publishing and bookselling industries, awarded 17 separate titles on Thursday night.
For the author of the cult children's series Harry Potter, the award went some way to making up for being pipped by poet Seamus Heaney to the Whitbread Book of the Year title last month.
Ferguson's trophy
Describing it as "an honour", Ms Rowling acknowledged that she was "terrified" coming onto the stage to collect her award.
"If you were all nine years old I'd feel so much more comfortable," she said.
She added that the "great thing" about collecting the award was that she didn't have to be photographed next to Jerry Hall, who was one of the Whitbread judges.
Manchester United coach Sir Alex Ferguson collected another trophy to add to his collection when his autobiography Managing My Life was voted Book of the Year.
Comedy veteran
Praising the writer Hugh McIlvanney, who turned Sir Alex's memoirs into a best-selling book, Sir Alex said: "If the truth be told, I wrote 250,000 words of drivel and Hugh brought some style and meaning to it."
Former Book of the Year winners include playwright Alan Bennett for Writing Home, Dava Sobel for Longitude, and Helen Fielding for Bridget Jones's Diary.
The Lifetime Achievement award went to comedy veteran Spike Milligan who said: "I thank you very much for this award and I think I deserve it."
Among the other top prizewinners was author Jacqueline Wilson who bagged the Children's Book of the Year Award for The Illustrated Mum.
Whilst TV's Naked Chef Jamie Oliver was beaten by fledging publisher Chris Stewart in the Newcomer of the Year Award.
Most the rest of the 17 titles went to top names in the book industry.
Book of the Year Award
Managing My Life by Sir Alex Ferguson
Author of the Year Award
JK Rowling
Children's Book of the Year Award
The Illustrated Mum by Jacqueline Wilson
Newcomer of the Year Award
Chris Stewart for his Sort of Books company and its first publication Driving Over Lemons
The Lifetime Achievement Award
Spike Milligan