The 12-year-old was denied a place at St Columbanus' College in Bangor, County Down, due to a cap on its intake of pupils with learning difficulties.
He had previously moved from a Catholic to a state-controlled primary school to ensure his needs were catered for.
He is set to gain a place at St Columbanus in September.
Counsel for the South Eastern Education and Library Board accepted it had misdirected itself in applying its entrance criteria.
Under the terms of an agreed settlement that authority is expected to acknowledge that any pupil who has at one stage attended a Catholic primary school is eligible.
The boy had moved schools in P4, because no Catholic school in his area had an appropriate specialist unit for his moderate learning difficulties.
His parents agreed to the switch recommended by a psychologist employed by the board on the basis that it was in his best educational interests, the court heard.
The boy's mother claimed she was told it would not affect his chances of getting into St Columbanus.
But a cap was said to have been put on the number of pupils with special educational needs the school can take in the transfer process.
With more applications last year than available places, an admissions criteria was used where preference was given to pupils from a Catholic maintained primary school.
The boy failed to get in on that basis, and a Special Educational Needs and Disability Tribunal upheld the decision.
His mother then issued judicial review proceedings against the board, claiming the criteria was unlawful.
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