JK Rowling missed out on a Whitbread Book Award nomination for her latest novel recently, after winning it last year with Harry Potter and The Prisoner of Azkaban.
The winner was chosen by a panel of child judges, selected by the children's programme from across the UK.
Writer and broadcaster Ian Hislop, on the panel which chose the shortlisted books, told BBC Radio 4's Front Row the winner was "beautifully and imaginatively written".
The book's author, Geraldine McCaughrean, said: "With a 10-year-old daughter, what awards could I have possibly won that would give me more pleasure?"
The shortlist of three books for the Blue Peter Book of the Year award also included JK Rowling's Harry Potter and the Goblet of Fire, and The Illustrated Mum by Jacqueline Wilson.
JK Rowling missed out on a Whitbread Book Award nomination for her latest novel recently, after winning it last year with Harry Potter and The Prisoner of Azkaban.
But despite the lack of critical acclaim from adult and child judging panels, Harry Potter and the Goblet of Fire is still breaking publishing records.
Blue Peter worked with the Scottish Book Trust to launch the awards earlier this year.
Nine child judges chose the winners in categories comprising The Book I Couldn¿t Put Down, The Best Book to Read Aloud and A Special Book to Keep Forever, as well as the best book award.
The shortlists, compiled from children's paperbacks published in the last year, were chosen by a panel including Mr Hislop, authors Malorie Blackman and Keith Gray, and Blue Peter editor Steve Hocking.
Mr Hocking said: "At a time of Harry Potter fever, it was great to see the range of winning titles."
Alan Yentob, director of BBC drama, entertainment and children's programmes, added: "The terrific response to these awards demonstrates that reading remains an important part of children's lives."