The watchdog's report was prompted by concerns raised last November by a number of the hospital's own doctors.
It looked at paediatric tertiary care services in the speciality areas of renal transplant, liver transplant, craniofacial surgery, neurosurgery, interventional radiology and cardiac services.
The Commission found that the Trust was struggling to meet rising demands, which led to delays in treatment and children being redirected to other services.
It makes a total of 12 recommendations to address issues including improving access to beds and giving better support to surgeons undertaking operations.
The Commission will oversee progress on the recommendations.
Anna Walker, the Commission's chief executive, said: "While we have no evidence of serious incidents causing harm to patients, the standard of care has not been as good as it should have been in some cases.The response to safety concerns has been slower than ideal."
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