Putting challenging pupils in isolation for extended periods at school can harm their mental health, the Centre for Mental Health (CMH) is warning.
The charity says the use of isolation rooms - and other restrictive interventions - can also "potentially drive even more challenging behaviour".
It says children who have already had traumatic experiences in their lives are especially vulnerable.
The government says it will publish new guidance for England by the summer.
The CMH says thousands of young people are subject to some form of restrictive intervention in schools in England every year for challenging behaviour.
There are no official figures on the numbers of children being put in isolation, but a BBC News investigation found that more than 200 pupils had spent at least five straight days in isolation areas in schools in England in 2017.
The CMH's report says these sorts of practices have a negative impact on a child's mental health, even if he or she has had no previous traumatic experiences.
But it warns that youngsters who have faced previous difficulties in life are "especially at risk of experiencing psychological harm".
"For example, exclusion and seclusion can echo relational trauma and systemic trauma; while physical restraint can echo physical and sexual abuse," the report says.
"As a result, these interventions may cause harm and potentially drive even more challenging behaviour."
The charity says a third of young people in England will have had a traumatic experience - such as the death of a close relative, being involved in a serious accident or experiencing violence or abuse at home - by the time they are 18.
It says all schools should be aware that these sorts of adverse events can traumatise children and should use a more compassionate approach to promoting good behaviour.
Its report highlights the need for "trauma-informed schools" which "actively seek to minimise the risk that they will add to their students' traumatic experiences".
In its response to Edward Timpson's review of school exclusions in England, published last year, the Department for Education said it would publish "clearer, more consistent guidance" on exclusions and behaviour by the summer of 2020.
"This includes guidance on managing behaviour, on the use of in-school units and the sorts of circumstances where it may be appropriate to use exclusion," it said.
In the meantime, the BBC has learned that families have taken legal action to challenge their children being placed in isolation for several days.
Dan Rosenberg, from Simpson Millar solicitors, who represents some of those families, said: "Isolation is being used as a dumping ground for some children - those with underlying difficulties are worst affected.
"Poorly behaved children will sometimes need to be removed from class at short notice, both by way of sanction and to enable them to calm down or for the lesson to continue.
"But deliberately putting children in isolation for extended periods of time is not an appropriate way to provide education or safeguard their mental health."
A Department for Education spokeswoman said: "Schools need to be safe and calm environments with effective behaviour management policies and approaches that meet the needs of all pupils.
"Restraint or restrictive intervention should always be a last resort and should be used in an appropriate way, with the pupil's best interests at heart."