The 31-year-old’s death follows allegations on social media that a pupil had hit the man with a chair last week.
The body of the teaching assistant, who has not been formally named, was discovered on Sunday in the Brackla area of Bridgend, police have told Sky News.
He worked at Ysgol Bryn Castell School in Bridgend, which was closed on Monday.
South Wales Police have not given a cause of death, but said a post-mortem found “no evidence to suggest an assault or injury”.
Officers are investigating and they have confirmed an inquest into the death will be held.
A Welsh Ambulance Services NHS Trust spokesperson told Sky News: “We were called on Sunday 1 December at approximately 8.47am to reports of a person needing urgent medical attention in Brackla, Bridgend.
“We responded with one rapid response vehicle and one vehicle from our hazardous response area team.”
Ysgol Bryn Castell School said on Twitter: “Apologies, due to unforeseen circumstances, YBC is closed for all pupils on Monday 2nd December 2019.”
Councillor Charles Smith, cabinet member for education and regeneration at Bridgend Council, told Wales Online: “There was an incident with a pupil earlier in the week and the teacher has died later.
“The school is closed today while investigations are made and police are involved.
“Our first concern is the welfare of the teacher’s family. Pupils are getting support.”
The local council said it was aware of the death.
Sky News has approached the school for comment.
The school is described in its prospectus as “a community day special school, which provides education for pupils aged 7 to 19 years old with complex emotional, social and behavioural special educational needs alongside specific learning difficulties and other additional learning needs”.
As of January 2019, the school had 147 pupils.