It ruled that Tower Hamlets council had acted unlawfully when it gave the go-ahead for the business to open close to Bishop Challoner School in Shadwell.
Apparently, members were wrongly directed not to take account of the school's proximity. The east London council now has to reconsider the application.
Councillor Peter Golds, leader of the council's Conservative group, said later: "This is a very important High Court decision.
"It clarifies the law and sets a benchmark that will enable local authorities everywhere to take account of health and well-being, particularly of schoolchildren, as factors in determining planning applications."
Both the school, which has 1,700 pupils, and many local residents objected to the change of use of a former grocery store into a takeaway.
Mr Justice Cranston said when the application for a hot-food takeaway was granted by the council's development committee in April, an officer's report specifically advised council members that the proximity of the proposed fast food outlet to the school could not be a "material planning consideration".
Richard Harwood, appearing for the council, had argued that at the committee meeting itself the close proximity of the school had in fact been treated as a relevant issue and taken into account.
Rejecting the submission the judge said the officer's report was "a clear direction to the effect that the points about proximity could not be given any weight at all".
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