U.S. District Judge Emmet Sullivan said the parties in the case, the State Department and conservative watchdog group Judicial Watch, also struck an agreement about the scope of the testimonies that some of Clinton's former top aides will give in the case.
Those testimonies, known as discovery, will take place over the next eight weeks and may yield information that would require Clinton herself to be deposed, Sullivan said in an order.
Clinton has come under fire for using a private email account and server at her home in New York state for official emails when she was America's top diplomat between 2009 and 2013.
Critics, including likely Republican presidential election rival Donald Trump, say she endangered government secrets and evaded transparency laws but the former first lady denies any wrongdoing.
Judicial Watch brought a lawsuit against the State Department to gain access to records related to a Clinton aide's employment. The Federal Bureau of Investigation is also probing her email arrangement.
"This is a very great victory for transparency and, despite the best efforts of the Obama administration and the Clinton camp, it looks like we might finally get some answers under oath about the Clintons' illicit email system," said Tom Fitton, president of Judicial Watch.
Sullivan gave Judicial Watch permission to take testimony from close Clinton aide Huma Abedin and others.
They may be asked about the creation and operation of the private server but nothing unrelated to "whether State conducted an adequate search" in response to Judicial Watch's request for the emails, according to the court order.
It is not typical for a judge to grant discovery to a plaintiff in a Freedom of Information Act case, but Sullivan said in the order that the question remained whether the State Department provided all relevant documents to Judicial Watch.
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