Because of the issues of military control of Davis' imprisonment, Chase refused to issue a writ of habeas corpus in June 1866, but almost a year later, in conjuction with an order to the military authorities from the president, a writ of habeas corpus brought Davis to Richmond to be transferred to the authority of the federal courts. He appeared before Underwood on May 13, 1867, bail was set at $100,000, and the bond was immediately posted. "Deafening applause" broke out in the courtroom when Davis was freed. Horace Greeley, one of a growing number of northerners who wanted the case settled so the country could get on with the healing process, had secured backing for the bond and personally guaranteed a quarter of it. He was in the courtroom that day and met Davis after his release.

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Major developments in the case are traced in the Jefferson Davis Chronology.