Fanny is a novel of ideas as well as an exuberant recreation of eighteenth-century picaresque style. Like the young protagonists of fiction written during the Age of Reason, Fanny searches for the meaning of life. She speculates irreverently on philosophical systems which consider only the behavior of men towards one another and notices the gap between the Alexander Pope's elevated sentiments and his personal lechery. The book's feminist themes are expressed by shifting perception so that the matter of human life is filtered through a woman's consciousness. Since Fanny notices that her own behavior changes when (for the sake of protection) she wears men's clothes and the book's most satisfactory male characters are bisexual, the story implicitly endorses an androgynous ideal and a social system in which neither sex has dominion.

The book's second major theme is its rehabilitation of witchcraft as a religion in which women are bound to the Goddess for the service of other women. The novel's witches preserve herbal lore, heal the sick, aid the abused, bring crops to harvest, and — most prominently — understand the birthing of babies. The thematic emphasis on the witchcraft's matriarchal nature provides an alternate vision of the philosophy, science and society that might follow from the worship of a goddess of life.