Churches won back the right to hold services in the city's public schools when a federal judge issued an injunction Friday against its no-worship policy.
The city said it would immediately appeal, guaranteeing that a case that has gone back and forth for 17 years will continue.
District Judge Loretta Preska ruled in Manhattan that a tiny evangelical Christian church, the Bronx Household of Faith, has a good chance of ultimately winning its lawsuit claiming the policy violates freedom of religion.
City lawyers had argued that the church's use of a public grade school ran afoul of the First Amendment's Establishment Clause, the prohibition against governmental endorsement of religion.
But the judge said, "In this court's view, losing one's right to exercise freely and fully his or her religious beliefs is a greater threat to our democratic society than a misperceived violation of the Establishment Clause."
A Bronx Household lawyer, Jordon Lorence, said the church welcomed the latest decision.
"The city can't single out religious expression and treat it worse than the expression of everybody else," Lorence said in a statement. "The court's order allows churches and other religious groups to meet in empty school buildings on weekends just as non-religious groups do while the lawsuit proceeds."
The judge had issued a similar temporary injunction last week, but the city appealed and the 2nd Circuit Court of Appeals narrowed it to cover only the Bronx Household of Faith, not the 50 or so other congregations that were worshipping in city schools until this month.
The city had begun revoking the churches' permits after an earlier 2nd Circuit decision upheld the no-worship policy and the U.S. Supreme Court decided against hearing the case.
As the appeals and injunctions continued, churches had to scramble for permits to worship in schools, then try to find space elsewhere.
City lawyer Jane Gordon promised another appeal, saying Friday's injunction was "inconsistent with the recent Second Circuit order and that court's prior decision on the case's merits."
The city said it would consider pending applications from churches for school space this weekend.
Associated Press writer Jim Fitzgerald contributed to this report.