The blood clot stemmed from a concussion she sustained while battling a stomach virus.
The illness has kept her out of the public view since Dec. 7.
A spokesman for Clinton said in a statement: "Her doctors will continue to assess her condition, including other issues associated with her concussion."
Clinton's doctors released a statement: "In the course of a routine follow-up MRI on Sunday, the scan revealed that a right transverse sinus venous thrombosis had formed. This is a clot in the vein that is situated in the space between the brain and the skull behind the right ear. It did not result in a stroke, or neurological damage. To help dissolve this clot, her medical team began treating the Secretary with blood thinners. She will be released once the medication dose has been established. In all other aspects of her recovery, the Secretary is making excellent progress and we are confident she will make a full recovery. She is in good spirits, engaging with her doctors, her family, and her staff," said Dr. Lisa Bardack, and Dr. Gigi El-Bayoumi.
Earlier this month, Clinton fainted and hit her head after contracting a stomach virus. Aides said she became dehydrated, then fainted, fell and hit her head. She was diagnosed with a concussion Dec. 13.
Clinton's illness led her to cancel an overseas trip and scheduled testimony before Congress about the attack on the U.S. Consulate in Libya.
The Associated Press contributed to this report.