The Child Brain Injury Trust said many families felt they had been "abandoned" by health and social services and received "little support or understanding" from education.
Its report, Scotland's Invisible Children, said the majority of children who suffered acquired brain injuries would experience long-term problems.
It recommended that policies should ensure that ongoing support is provided to families through a care manager based in health or social services departments.
The charity also said the Scottish Executive should allocate more resources to developing services specific to acquired brain injury and that training was needed among professionals in all agencies.
And the recording of child brain injury in Scottish accident & emergency departments must be standardised if its true extent is to be recognised, it added.
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