The woman had sued state and municipal governments in October 2005 using the pseudonym Jane Doe. She had alleged physical and sexual assault in violation of her constitutional rights, the appeals court said.
A federal judge in Syracuse had concluded that the state's rape shield law, which protects the identities of possible rape victims, does not provide for the use of pseudonyms, a finding that led to the dismissal of the case.
But the Manhattan appeals court said the decision was wrong.
"In light of the nature of plaintiff's claims - including physical and sexual assault - the district court should have afforded plaintiff wider latitude in pressing her claims," the appeals court said.
A three-judge panel said judges must balance the interest of someone bringing a lawsuit to remain anonymous against the public interest in disclosure and the potential prejudice to defendants if a plaintiff is allowed to proceed under a pseudonym.
It was impossible to get reaction to the ruling because the plaintiff and defendants remained anonymous and the appeals court unsealed just enough of the record so it could write about its findings.
The appeals court said the woman had asked the judge presiding over the case to let her obtain the evidence necessary to identify certain John Doe defendants.
The woman said the defendants had refused to comply with identification requests in the case and had retaliated against her for seeking the names of her assailants, the appeals court said.
The woman also had requested a restraining order to protect her from defendants' "terror campaign (in retaliation) for speaking out and filing a complaint," it said.
The lower-court judge, who gets the case back, had rejected those requests as well.
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