The court has barred pupils from appealing against the judgments of the Special Needs Tribunal, saying their parents must do so instead. But it is only the children, not their parents, who will get legal aid.
Special needs campaigners say it leaves most families unable to fight for their children's needs, particularly in the face of council lawyers.
The judgment has also alarmed special needs advocates by deciding that the "efficient use of resources" - the cost of helping a child - is more important than the pupil's right to have its needs fully assessed and met.
This was the first appeal against a decision by the tribunal, which was set up under the 1993 Education Act as a fairer way of complaining about LEA decisions.
One current case involves a dyslexic child from the London borough of Westminster who wishes to go to a specialist, private school in Sussex. The borough disagrees, arguing that Pimlico School can cope with the child's requirements and that the additional cost of a private placement - about Pounds 10,000 a year - is not justified.
The tribunal and now the High Court have agreed with Westminster. The High Court dismissed the child's case arguing firstly that the parents, not the child should have applied; and secondly that the LEA is entitled to argue its case, in part, on grounds of cost.
If the High Court decision stands it marks a major change from recent years. The 1990s have seen an exponential growth in the number of legal challenges about special educational needs, fuelled to a large extent by a child's ability to get legal aid in his or her own right.
The child's solicitor, Jack Rabinowicz, said: "If children are no longer able to take such cases it means that only such parents as qualify for legal aid will be appealing.
"And then, when there's a dispute over integration and non-integration the local authority's resources will be taken into account. Special needs decisions will therefore be resource-led rather than needs-led. So the whole problem of the 1993 Act not being child-centred is reinforced and exacerbated."
The decision could be overturned, however, as the judge granted leave to appeal.
Jessica Saraga, the tribunal secretary, said that the concerns were largely technical as parents can only appeal to the High Court on points of law. She said that the decisions of the tribunal, which costs nothing to attend, should be regarded as final.