The couple has applied to the High Court in an attempt to force the school – the only one of its kind in the country – to reverse its ban on their daughter wearing a hijab.
The girl's parents were so incensed at the decision that they have pulled their child out of St Cyprian's Greek Orthodox Primary Academy, in Thornton Heath, the Daily Mail reported.
The school, however, is determined to fight attempts to overturn the ban on the pupil wearing a hajib.
Head teacher Kate Magliocco said the uniform policy was made clear to the parents when the girl arrived in Year 3.
It was not until she moved into Year 5 in September last year that they wanted their daughter to start wearing a hijab, a traditional headscarf worn by Muslim women which represents the Islamic principle of modesty.
"The decision not to allow her to wear a headscarf was taken by the governing body. The school has a very particular uniform policy which is shared with parents and, as head, I must follow the plan," Magliocco said.
The girl's parents complained to the governing body, which upheld the ban with the support of the Archdiocese of Thyateira and Great Britain.
Her parents want her to return to St Cyprian's as her brother still attends the school.
The family have submitted a fresh application to have the issue heard at the High Court after their first attempt was rejected. The matter is due to be considered in February.
A spokesman for the Archdiocese of Thyateira and Great Britain said it would not be "appropriate" to comment.
There is no mention of a ban on headscarves in the uniform policy on the school's website.
Girls are required to wear a dark blue coat, an optional blazer, a skirt, a white blouse, a navy blue pullover and navy blue or white socks and black shoes.
Shuiab Yusaf, trustee of Croydon Mosque and Islamic Centre, urged the school to reconsider the ban.
"We encourage schools to be a little less strict and allow Muslim girls to wear headscarves if that is what they want to do," Yusaf said.