She joins a distinguished line of past winners including Ted Hughes, Jacqueline Wilson, Anne Fine and Philip Pullman.
Chair of judges, Julia Eccleshare, said: "It's relatively rare for a book late in a series to win a major prize, but the Chronicles of Ancient Darkness is such a towering achievement, as a whole as well as in terms of the individual books, that it was our unanimous choice."
The Guardian Children's Fiction Prize was founded in 1967 and is unique in that it is judged by children's authors themselves, and no one can win it more than once.
This year's panelists were Linda Buckley-Archer, Jenny Downham, and last year's winner Mal Peet.
The judging process was shadowed by young critics, who described Ghost Hunter as "a thrilling story of love, friendship and terrifying evil" and "the perfect book for anyone who likes adventure, prehistory and survival".
Michelle Paver told the Guardian that she had prepared her "loser's face" after being warned that series books never won prizes. She was particularly pleased to win for this final book in the series, "because my aim was to write six really good books and not have the thing tailing off".
The series is set in prehistory and tells the story of a boy Torak, his female friend Renn and his lupine companion Wolf. Research for Ghost Hunter took Paver to Finnish Lapland, where she snowshoed on the trail of elk and reindeer, and to the UK's Wolf Conservation Trust, where she learnt to "speak wolf".
Extracts from some of the winning entries to the Guardian Young Critics competition, reviewing all eight books longlisted for the prize, will be published in Education Guardian on Tuesday 12 October.
