The Sandman creator was presented with the prize for his recent The Graveyard Book. The awards were presented last week during the 67th World Science Fiction Convention in Montreal, Canada.
The children's fantasy book tells the story of a boy named Nobody Owens, who is raised by the occupants of an old, ornate graveyard after the murder of his parents.
Girl Genius, volume eight, by Kaja and Phil Foglio took the Hugo Award in the best graphic story category, fighting off competition from DC and Dark Horse titles.
Named after Amazing Stories founder Hugo Gernsback, the Hugo Awards have been presented annually since 1955, recognising outstanding achievement in the science fiction and fantasy genres.