The two women alleged that when the CQC inspected and registered the Gender Plus clinic it did not take this into account
NHS guidance says all young people, who are recommended for hormone interventions, must have the decision reviewed and endorsed by a national multi-disciplinary team that can consider all aspects of their care.
Gender Plus Hormone Clinic, which was set up by Dr Aidan Kelly and is led by nurse consultant Paul Carruthers, had told the court it follows the NHS guidance and had set up its own multi-disciplinary team. Its procedures were reviewed by the CQC inspectors.
In the ruling, Mrs Justice Eady said: "I am satisfied the steps taken by the CQC were rationally focused on scrutinising the actual process by which the clinic provided the service in issue. I duly reject this objection.
"What is, moreover, clearly apparent from the CQC's evidence is the detailed scrutiny that was undertaken in order to be able to assess clinic's compliance with the regulatory requirements.
"It is apparent that this was an assessment that drilled down to the detail of the service provided... with patient safety foremost in mind."
She said the question whether the CQC had adequately considered "the particular, and changing, approach adopted by the NHS", was important.
But she concluded the criticisms of the clinic were about the internal structure of the organisation and "focused on issues of form rather than substance".