Author Frances Hardinge said she was surprised and delighted to receive the 30,000 pound (USD 50,000) prize last night.
She said that "sometimes children's fiction is seen as a bit lightweight, in a way that I think is not deserved."
Open to writers form Britain and Ireland, the prize selects a champion from winners in five categories: novel, first novel, biography, poetry and children's book.
Hardinge beat Kate Atkinson's wartime novel "A God in Ruins"; Andrew Michael Hurley's debut horror novel "The Loney"; Andrea Wulf's biography of scientist Alexander Von Humboldt "The Invention of Nature"; and poet Don Paterson's "40 Sonnets.