In a letter to the government on behalf of 500 schools, the Boarding Schools Association said hotel accommodation was unsafe for pupils.
James Davidson said the thought of his daughter quarantining on her return to school from Abu Dhabi made him anxious.
The government said parents should accompany children during quarantine.
Kitty Davidson faces having to quarantine in a hotel for 10 days if she returns to Dauntsey's School in Wiltshire, due to the United Arab Emirates being on the government's travel 'red list'.
Mr Davidson said it has been an "anxious" and "unsettling" time.
"This is not something we really want her to go through," he said.
"Equally, it will be extremely tough on her mentally to be learning remotely whilst all her friends are in school mixing socially.
"The stance from the schools is that they can provide quarantine and will provide regular testing, so I am not sure this situation has really been thought through by the government."
Seventeen-year-old Saina Sodhi, who attends Millfield School in Somerset, said uncertainty over travel and quarantine measures meant she was unlikely to return from India.
"Parents will be extremely unsettled to have to make their child quarantine at an unsafe location abroad," she said.
"Having not been to school for a year, going back now is crucial as being away from school for longer will have its impact on my education and performance as a student.
"A majority of my peers, who I have been in touch with, were extremely excited to go back to school but will not be returning due to the quarantine hotels."
Emma Taylor, headteacher of Dean Close School in Cheltenham, said asking pupils to stay in a hotel was "unsafe" and Westonbirt School headteacher Natasha Dangerfield said the policy risked putting children off coming to the UK.
"Those students that are on those countries listed, they won't come back," said Ms Dangerfield.
"I don't think the children or their parents are prepared to put them in that position and that's a huge loss to their education."
The Department for Education said children were not exempt from quarantine and asked parents to consider if it was "essential" for their children to "travel unaccompanied into the UK at this time".
A spokesman said if travel was "unavoidable", a parent or family member must accompany their child during quarantine.
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