Researchers said seven in eight youngsters given the procedure were unlikely to benefit from the operation.
These “unnecessary” procedures are costing the NHS tens of millions of pounds a year, they added.
The most common reason for a tonsillectomy - the surgical procedure to remove the tonsils - is a recurrent sore throat.
Evidence suggests that the procedure results in modest, short-term reductions in recurrent sore throats in severely affected children, the researchers said.
UK guidelines suggest offering tonsillectomy for children with seven or more documented sore throats over the course of a year, they added.
But only a small number of those who received the procedure had this many sore throats, according to the study published in the British Journal of General Practice.
Researchers from the University of Birmingham analysed health records from more than 1.6 million children from 700 GP surgeries around the UK.
The data was collected between 2005 and 2016.
The authors found that most childhood tonsillectomies followed “non-evidence-based indications” - 12.4 per cent of those who had the procedure had five or six sore throats in the preceding 12 months and 44.6 per cent had between two and four sore throat episodes.
Almost one in 10 suffered just one sore throat before being offered the procedure.
Other “non evidence-based” reasons for youngsters undergoing tonsil removal included obstructive sleep apnoea and other sleep disordered breathing.
They concluded that 32,500 children - or seven in eight who have the procedure - who undergo a tonsillectomy in the UK each year are “unlikely to benefit” from the procedure.
“In the UK, few children with evidence-based indications undergo tonsillectomy and seven in eight of those who do (32,500 of 37,000 annually) are unlikely to benefit,” the authors wrote.
They said unnecessary tonsillectomies were costing the NHS across the UK £36.9 million each year.
Tom Marshall, professor of public health and primary care at the University of Birmingham, said: “Research shows that children with frequent sore throats usually suffer fewer sore throats over the next year or two.
“In those children with enough documented sore throats, the improvement is slightly quicker after tonsillectomy, which means surgery is justified.
“But research suggests children with fewer sore throats don’t benefit enough to justify surgery, because the sore throats tend to go away anyway.
“Our research showed that most children who had their tonsils removed weren’t severely enough affected to justify treatment, while on the other hand, most children who were severely enough affected with frequent sore throats did not have their tonsils removed.
“The pattern changed little over the 12-year period.
“Children may be more harmed than helped by a tonsillectomy.
“We found that even among severely affected children, only a tiny minority ever have their tonsils out.
“It makes you wonder if tonsillectomy is ever really essential in any child.”