The pupil, whose identity and gender are not being disclosed for legal reasons, studied at Al-Khair secondary school in Croydon, south London.
The parent of the pupil has attacked the policy of the private Islamic school as "nonsense", saying it meant students were not being prepared for life in British society.
"How are these kids going to integrate in the wider shape of society when they have to work in the same places that [people of the opposite sex] are working? This is totally nonsense," the parent told 'The Sunday Times'.
These require schools to teach pupils to live by British values, including respect for the law, democracy and the right of women to be treated on a par with men.
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The behaviour policy at Al-Khair secondary, which charges annual fees of 4,900 pounds per student, prohibits interaction "through any medium [eg: verbal, email, messaging, etc]" between male and female students who are considered "non-mahrams" (not close relatives).
Under a section of the policy outlining "high-level" offences that could lead to an exclusion, "free-mixing" is listed alongside "drug dealing, stealing, extortion, racism and arson".
While schools inspectorate Ofsted reviewed the school's behaviour policy during a snap inspection last September, the regulator failed to address the issue that relates to "free-mixing", or interaction between male and female pupils.
A spokesperson for the DfE said: "We are clear that gender segregation of this type has no place in our schools and that boys and girls must be allowed to communicate.