The case was brought by a London man, known only as Mr K, who wanted his daughter to attend one of the two girls' secondary schools in the borough of Newham.
The authority offered her a place at a mixed school, and an admissions appeal panel decided in the council's favour. But Mr Justice Collins ruled last week that by failing to take account of Mr K's beliefs, Newham breached the Human Rights Act.
The case represents the first successful challenge to school admissions policies under the Act, which gives a right to respect for religious and philosophical convictions.
Chris Lowe, legal consultant to the Secondary Heads Association, said: "Unless this is overturned on appeal, a large number of Muslim and other parents may well insist on a single-sex education for their children. That would result in some schools being 1,000 per cent oversubscribed, while others are vastly undersubscribed."
Eleanor Wright of the Fisher Meredith law firm, who acted for Mr K, said: "It's not clear exactly how much weight admissions authorities should give to religious conviction." She added that while it should not be the overriding principle, authorities had to take it into consideration.
At the very least parents should be informed that education authorities and appeal panels will take religious beliefs into account, Ms Wright said. It also means leaving a space on admissions forms where parents can say that they have religious reasons for preferring a particular school.
Unusually Newham gives priority to parents who express a preference for mixed or single-sex schools. But parents are not invited to explain their choice.
A Newham spokeswoman refused to comment on the case but said the council would be taking legal advice and considering its options once the full judgment is published. An appeal looks likely.