The judge, Emmet Sullivan, said Clinton will have to answer questions under oath from the group, Judicial Watch, within 30 days.
Separately, Sullivan denied Judicial Watch's request to depose an official in the State Department's Freedom of Information Act office, Clarence Finney, but approved their request to depose a former IT official, John Bentel.
Sullivan heard arguments on the deposition requests at a lengthy motion hearing in July.
At the time, he seemed skeptical that more substantive information could be gleaned from a deposition, given Clinton's numerous public statements on the subject of her email server, as well as her closed testimony to the FBI and open testimony to the House Select Committee on Benghazi.
"We are pleased that this federal court ordered Hillary Clinton to provide written answers under oath to some key questions about her email scandal," Judicial Watch President Tom Fitton said in a statement in response to Sullivan's decision. "We will move quickly to get these answers. The decision is a reminder that Hillary Clinton is not above the law."
Clinton spokesman Brian Fallon declared victory Friday and dismissed Judicial Watch as "a right-wing organization that has been attacking the Clintons since the 1990s."
"This is just another lawsuit intended to try to hurt Hillary Clinton's campaign, and so we are glad that the judge has accepted our offer to answer these questions in writing rather than grant Judicial Watch's request," Fallon said.
Clinton has repeatedly said she set up the private server during her tenure leading the State Department for convenience and wasn't attempting to evade FOIA, though she also called the decision "a mistake."
While Clinton is not a direct party in the FOIA lawsuit, her personal attorney, David Kendall, appeared at the hearing to argue that a deposition would be an exercise in futility, and insisted there's "not one scintilla of evidence on the central question of whether there was intent to thwart FOIA."
Michael Bekesha, the lawyer for Judicial Watch, insisted there were outstanding questions that only Clinton could answer about why she set up the server, and argued there would be value in having her testify to those motivations under oath.
They had asked for a three-hour window to question her, less than the seven hours they were given to question several current and former State Department officials last month.