e decision is understood to have been taken by Nigel McQuoid, head of King's academy, Middlesbrough, last year after a meeting between library and English staff.
Discussions on what should be included in the library when the new school, which is sponsored by a Christain evangelist, opened in September 2003 broke down after a disagreement over the best-selling wizard stories.
Some had felt that JK Rowling's books were merely innocent whimsy, while others worried that they might lead pupils into the world of witchcraft and the occult.
Apparently anxious to avoid a damaging internal row, management stepped in.
There is no formal ban and pupils can bring their own copies of Harry Potter into school for private reading. But the novels are not stocked in the library.
The academy is sponsored by the Vardy Foundation, founded by multi-millionaire Christian evangelist, Sir Peter Vardy. It shares its headteacher, Mr McQuoid, with its sister school, Emmanuel college, Gateshead, which hit the headlines in 2002 when it emerged that staff were teaching biblical creationism alongside evolution.
Asked whether his decision on Harry Potter would deprive students who did not have access to the best-selling novels at home, Mr McQuoid said: "The world's best seller is the Bible and I would be interested to see if every school in the country has a Bible.
"As far as the education of young people is concerned, some critics have said they don't think the Harry Potter books are particularly well written."
Marilyn Mason, British Humanist Association education officer, said: "Why pick on Harry Potter? Has the school refused to stock all fantasy and fairy tales on its shelves? And if so, what a deprivation for its students, who probably, unlike the teachers, can tell fact from fiction. A more self-confident school would be happy to allow these things."
Mr McQuoid said Harry Potter books were not in the library because there was no staff unanimity on the issue.
"The decision was made in the interests of team unity and was not on the literary merits or otherwise of Harry Potter," he said.