The five-year-old's mum says the boy was "tortured and tethered like an animal" at the special school in Northern Ireland.
She claims her "placid" son's behaviour had "suddenly" changed over the course of a year and he had panic attacks when she tried to sit him on a chair.
But she was horrified to discover photos of the lad, who has no physical disability, strapped to chair by his waist, legs and ankles.
She told Belfast Live: "He was so distressed and agitated, having panic attacks, suffering night terrors and he was tearful and acting very strangely, a totally different little boy to the one we knew and he couldn't tell us why."
In January this year, she looked through photo scrapbooks from the school and noticed he had been restrained in a chair usually used for children who "need to be elevated and angled" to the right position.
The mum explained: "I was talking away to him and asking him what he wanted to show me, and he just kept touching the book.
"I started looking very closely at the photos and my heart just started racing. It was there in plain sight, my wee man strapped into a chair by his ankles.
"I felt sick, it was like the fog lifted. Now we knew, now we had an explanation."
She has now made a complaint to the Education Authority and the Department of Education citing negligence and breach of duty by the school.
Police Service of Northern Ireland also confirmed they were investigating.
The Education Authority (EA) said: "In order to protect the confidentiality of the child, EA cannot comment on circumstances relating to specific children."
While a National Association of Head Teachers spokesperson, representing the school's principal, said: "There is an ongoing investigation into these allegations. Our member is complying fully with the investigation."
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