With a recent survey suggesting almost 50% of children with Attention Deficit Hyperactivity Disorder have been excluded at some point, parents face difficult choices.
Up to one in 20 children have ADHD, which affects concentration and can cause them to be disruptive.
Many are being put on medication but unions warn that some schools cannot meet their medical needs.
And American scientists have raised concerns about the widespread use of ADHD medications.
A recent survey by the National Attention Deficit Disorder information and support service found the exclusion rate for children with ADHD was 10 times higher than that of those without.
Some parents have told the BBC they were told to give their children medication or keep them at home, and that they often felt they were being denied a proper education.
The National Association of Head Teachers spokesperson, Jan Myles, said: "It's the system that fails the child but all too often the blame is laid at the door of the school.
"A lot of heads I'm talking to on a daily basis are exhausted with trying to implement different strategies that are not working."
One mother, Linda Sheppard, is taking her local authority to the European Court of Human Rights to gain her son the educational support she claims he needs.
Ms Sheppard removed her son from his school because she says they were unable to offer him adequate support in the classroom.
Continual exclusions from school trips and other activities caused his well-being to plummet and by the time he was seven he threatened suicide, she says.
For 18 months Ms Sheppard struggled to find a school she felt could cope with her son's education needs.
"It's ridiculous - the only way parents can get their children an education is through the courtroom," says Ms Sheppard, who claims that many exclusions are not recorded in official statistics and are classified as authorised absences by schools.
Other parents say they are coming under pressure to have their children on prescription drugs.
The BBC's Five Live Report spoke to one parent who said they were asked by their school to either put their child on medication or they would be excluded.
In the past 10 years the prescription rates for ADHD medications, which are based on the chemical methylphenidate, have risen sharply.
In 1994 there were just 4,000 prescriptions for methylphenidate, 10 years later that figure had gone up to 359,000 - a 90-fold increase.
However, the news comes at a time when leading American doctors have called for greater warnings on the labels of the ADHD medications.
The risks outlined by Dr Steven Nissen include tics, strokes, and in severe cases, sudden death.
"These drugs are not candy," says Dr Nissen, President of the American College of Cardiologists who was one of the key experts that moved to increase the warnings. "These are powerful medications that have serious risks."
In Britain though the drug advisory board, the MRHA, is not yet planning to release any new guidelines.
Manufacturers said the risks identified were small and only applied to people with pre-existing heart conditions.
One drugs company, Novartis, said it had "conducted a review of our global safety database in early 2005 which did not show any increased events of sudden deaths or strokes among methylphenidate users compared to the general population".