The Education Authority (EA) breached the human rights of two disabled pupils, according to court declarations agreed during judicial review proceedings.
One of the pupils was prevented from attending school for long periods and access was hindered for the other.
It was found both pupils were "treated differently to other children in the state" because of their disability.
The EA said it would "take on board all learnings from these cases".
The legal action was brought by the Children's Law Centre (CLC), acting on behalf of the pupils.
