Pullman is a supporter of the British Humanist Association and an Honorary Associate of the National Secular Society. New Yorker journalist Laura Miller has described Pullman as one of England's most outspoken atheists; Pullman describes himself as being an agnostic atheist.
On 15 September 2010, Pullman along with 54 other public figures signed an open letter, published in The Guardian newspaper, stating their opposition to Pope Benedict XVI being given "the honour of a state visit" to the UK, arguing that he has led and condoned global abuses of human rights. The letter says "The state of which the pope is head has also resisted signing many major human rights treaties and has formed its own treaties ("concordats") with many states which negatively affect the human rights of citizens of those states". Co-signees included Stephen Fry, Professor Richard Dawkins, Terry Pratchett, Jonathan Miller and Ken Follett.
Literary critic Alan Jacobs (of Wheaton College) said that in His Dark Materials Pullman replaced the theist world-view of John Milton's Paradise Lost with a Rousseauist one. Donna Freitas, professor of religion at Boston University, argued on BeliefNet.com that challenges to traditional images of God should be welcomed as part of a "lively dialogue about faith", and Rowan Williams, the Archbishop of Canterbury, has proposed that His Dark Materials be taught as part of religious education in schools. The Christian writers Kurt Bruner and Jim Ware "also uncover spiritual themes within the books." Pullman has also referred to himself as knowingly "of the Devil's party", a reference to William Blake's revisionist take on Milton in The Marriage of Heaven and Hell.
Pullman's latest novel, a contribution to the Canongate Myth Series, is The Good Man Jesus and the Scoundrel Christ. It is "a far more direct exploration of the foundations of Christianity and the church as well as an examination of the fascination and power of storytelling."
The His Dark Materials books have been criticised by the Catholic League for Religious and Civil Rights and Focus on the Family. Peter Hitchens has argued that Pullman actively pursues an anti-Christian agenda. In support of this contention, he cites an interview in which Pullman is quoted as saying: "I'm trying to undermine the basis of Christian belief." In the same interview, Pullman also acknowledges that a controversy would be likely to boost sales. "But I'm not in the business of offending people. I find the books upholding certain values that I think are important, such as life is immensely valuable and this world is an extraordinarily beautiful place. We should do what we can to increase the amount of wisdom in the world".
Peter Hitchens views the His Dark Materials series as a direct rebuttal of C. S. Lewis's The Chronicles of Narnia; Pullman has criticized the Narnia books as religious propaganda. Both Pullman's and Lewis's books contain religious allegory that features talking animals, parallel worlds, and children who face adult moral choices that determine the ultimate fate of those worlds.
Christopher Hitchens, author of God Is Not Great, praised His Dark Materials as a fresh alternative to C. S. Lewis, J. R. R. Tolkien and J. K. Rowling. He described the author as one "whose books have begun to dissolve the frontier between adult and juvenile fiction."