For the independent school, which attracts physically disabled pupils from both sides of the Irish border, still needs Pounds 29,000 if it is to re-open in September.
Mr Justice Kerr, in his judgment, said it was not unreasonable for the Northern Ireland education department to refuse to fund the school but criticised one of its inspectors who told parents and officials of the trust he had "better things to do" than inspect an independent school.
The judge said they were ill-judged remarks which had created a suspicion of bias among parents and were at best ill considered.
Now, after two further inspections, the department has agreed to provide funding for pupils' fees.
A spokesman said the school curriculum had improved sufficiently to warrant the final registration, but there were still deficiencies.