The Disabilities Commissioner, Paul Gibson, said it too had become involved because access to education was a fundamental human right.
"This case raises the legal issue of the obligation for New Zealand schools to reasonably accommodate the needs of students with disabilities," he said.
The boy in this case was 14 when he was expelled from Green Bay High School in 2013.
He has since left Auckland, and is no longer in mainstream education.
Principal Morag Hutchison declined to comment on why it wanted the boy to remain barred. Board of trustees chairman Norman Wallace did not return calls from the Herald of Sunday.
Jen Puah from Aotearoa Youth Law - who is representing the schoolboy in the court action - said the teen wanted to return to the West Auckland school.
But the school had made it "extremely difficult" for that to happen.
Puah said the case reflected a large number of schoolchildren slipping through the cracks, partly because schools were dealing with stretched finances and were unable to meet all the needs of students with behavioural issues.
IHC director of advocacy Trish Grant hoped the case would lead to stronger legislative protection for students with disabilities.
Students with disabilities had the same right as their non-disabled peers to be enrolled and receive an education, but she said there wasn't a law that protected them from being rejected through disciplinary or enrolment processes, or restrictions placed on the time they're at school.
"We know there's not enough clarity about what is reasonable accommodation," she said.
"When we look at what happened from when he began to when he exited, we see patterns that are replicated with other young people."
Living with Asperger's
• Asperger's syndrome is characterised by a range of behavioural problems including difficulty communicating and having fixated interests and repetitive behaviours.
• Treatment includes social and communication skills training, applied behaviour analysis and cognitive behaviour therapy for anxiety and depression.
• An estimated 8500 Kiwi children have Asperger's.
• It is present from birth, and becomes more evident in early childhood.