Proposals for the City of London academy, due to open in September, initially included pupils from nearby Hackney. But after a consultation, managers changed the boundaries, giving Islington children first refusal.
The union fears this will mean children from gentrified areas of Islington will be given places at the expense of poorer children on adjacent Hackney council estates.
At the academy's predecessor school, Islington Green, 30 per cent of children come from Hackney. But only 10 Hackney children will be given places if the new academy is oversubscribed.
Hackney is one of England's most deprived boroughs. More than half of its secondary school children speak English as a second language.
"It's a complete abuse of the consultation process and will unfairly disadvantage these children," an NUT spokeswoman said.
But Paul Curran, director of children's services for Islington, said: "I'm confident the consultation was open and inclusive, and that the academy is the right move for the future of Islington."
Organisers of the Thomas Deacon academy in Peterborough were reprimanded earlier this year by the Commission for Racial Equality, for excluding a predominantly Pakistani district from the school's target area.
It is not yet known when the judicial review for the London academy will come to court.