Pupils returned to Movilla High in Newtownards on Monday, three weeks after a high-profile strike by teachers began.
The 539 schoolchildren who are taught at the high school began to arrive at the gates shortly after 8am.
However, the pupil at the centre of the storm will not return to class until an independent assessment has been carried out on his needs.
A deal was brokered between the NASUWT teaching union and the South Eastern Education and Library Board last Thursday, after weeks of bitter confrontation between the two sides.
The union has suspended its strike action, but has reserved the right to return to the picket-line if the terms of the deal are not honoured.
The teachers began their strike after their pay was docked when they refused to teach the pupil at the centre of the storm.
Sonya Boal was among the parents dropping children off at the school on Monday. Her two daughters are aged 12 and 16. She said: “I am glad they are back at school today, especially because my eldest daughter is doing her GCSEs this year.
“It has been a bit hectic with them being off school for so long. The teachers must have had good reasons for going on strike, but I hope that it doesn't ever happen again.”
Education Minister Caitríona Ruane welcomed the deal and thanked the parents involved for helping to move the dispute forward.
She said: “My Department is currently in the process of identifying an independent assessor to assess the educational needs of the individual pupil. The assessment will commence as soon as possible and I hope we are now nearing the end of this dispute.”
The SEELB also welcomed the settlement.
“We are very pleased this has come to an end,” a spokesman said.
Peter Scott from NASUWT said the matter could have been sorted out much sooner.
“We welcome the fact this has been resolved, but it's just a pity it took so long," he said.