Tavistock and Portman NHS Foundation Trust has been told to shut the clinic by spring after it was criticised in an independent review.
Instead, new regional centres will be set up to "ensure the holistic needs" of patients are fully met, the NHS said.
The new centres - one based in London and the other in the north west of England - should be fully open in spring 2023 and would run in conjunction with leading children's hospitals, including Great Ormond Street and Alder Hey
LGBT rights group Stonewall said it was pleased the NHS was addressing "unacceptable" waiting times faced by young trans people trying to access gender-identity healthcare.
A Stonewall spokesperson said: "The creation of new specialist regional centres in London and Manchester next year, with more to follow, will go some way to addressing the strain experienced by having just a single, centralised service."