There was not enough evidence about either how safe they were to take or whether they were clinically effective to justify prescribing them to children and young people who were transitioning, it added.
The government welcomed NHS England's "landmark decision", which it said was "in the best interests of children".
NHS England made the announcement in response to the results of a public consultation on the ban, which it first proposed last June, and a review of available evidence by the National Institute for Health and Care Excellence (Nice).
A spokesperson said: "NHS England has carefully considered the evidence review conducted by Nice and further published evidence available to date. We have concluded that there is not enough evidence to support the safety or clinical effectiveness of puberty suppressing hormones to make the treatment routinely available at this time."
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