Hundreds of pupils spent at least a week in isolation booths last year, according to a new investigation into the controversial practice.
More than 225 pupils in England spent five consecutive days in school isolation booths, including one child who claimed to have spent three months in a classroom on his own.
One school had five separate isolation rooms, each permanently staffed, at an annual cost of more than £170,000, BBC News has found.
Two schools – which included toilets as part of their facilities – did not allow pupils to leave the unit all day.
Some 5,000 children with special educational needs attended such rooms last year, dozens of which had complex needs.
Isolation rooms are facilities that pupils are sent to when it is thought that they need to be removed from a classroom during the school day.
Some schools use "seclusion" units where children remain on their own, while others place pupils in more conventional classrooms to work in silence.
Behaviour consultant Paul Dix said that he’d seen 50 children at one time in isolation in one school, and also met one child who had spent 36 days in isolation in one school year.
Speaking to BBC News, he said: “That is not education, it is a custodial sentence.”
The independent adviser on behaviour to the Department for Education, Tom Bennett, said isolation could be effective in tackling disruption in classrooms.
The national broadcaster's investigation used collected data from about 600 schools across the UK. It found that more than 200 schools in England used isolation, compared with 12 in Wales, six in Scotland and none in Northern Ireland.
The DfE said children should be placed in isolation for no longer than is necessary, and that the health, safety and welfare of pupils must always be put first.
A DfE-commissioned report last month found that most secondary schools are using “internal inclusion units" to deal with difficult pupils, as an alternative to exclusion.