The rise has been most sharp in the northwest of England, where the number of exclusions has doubled since 2011.
Every part of England has also seen significant increases.
The research by the charity Ambitious about Autism found 4,485 children who are on the autism spectrum were excluded either permanently or for a fixed period in 2015/16.
Chief Executive Jolanta Lasota said: “The impact of these exclusions can’t be underestimated – not only do children fall behind academically, but the isolation from their peers creates deep unhappiness, social anxiety and mental health problems.
“Our evidence clearly shows children with autism are disproportionately at risk from exclusion, compared to other pupils.”
Violent or disruptive behaviour in classrooms is a huge problem for many teachers and exclusions are normally a last resort.
The charity believes though that occasionally autistic children, and those with other special needs, have been unfairly kicked out of schools.
At Shavington Primary school near Crewe in Cheshire they have worked hard to create an environment that allows students with autism to flourish and aims to prevent meltdowns before they happen.
Lewis Robinson, 10, doesn’t tend to have violent episodes, but he can sometimes be quieter and withdrawn. He does have the support of the teaching staff and crucially his classmates.
He’s also helped by his sidekick, a hand puppet called Summer, that he fiddles with in class to reduce his anxiety.
Julia Gawn, special educational needs coordinator at the school, explained: “When he is feeling anxious he knows he has got somewhere calm that he can go to so that those anxieties don’t overcome him and lead to meltdowns.”
“In the time he has been here he has gone from a very shy child who wouldn’t interact with anybody strange coming in… to a child who will completely and utterly engage in activities at his level with support.”
Many other schools have complained about funding cuts that have damaged their ability to support children with special educational needs but the Department for Education insists investment is at record levels.
Minister for children and families Nadhim Zahawi MP said: “Thanks to this government’s reforms, more children and young people with special educational needs and disabilities are getting the support they need at school and college, and the number who move on to training schemes, apprenticeships or supported internships is increasing.
“We know more needs to be done to make sure that vulnerable children are not unfairly treated.”
A review is now underway looking at why children with autism are more likely to be excluded than others.