The clot did not result in a stroke or neurological damage, they said.
The clot, or thrombus, was discovered during a routine MRI Sunday as Clinton was recuperating from a fall and concussion, a statement from spokesman Philippe Reines and Clinton's doctors said.
"The scan revealed that a right transverse sinus venous thrombosis had formed," the statement said, explaining Clinton's clot formed in a vein "in the space between the brain and the skull behind the right ear."
Drs. Lisa Bardack and Gigi El-Bayoumi said Clinton was on blood thinners and would be released after her medication regimen is established. They didn't say when they expected that would be.
"In all other aspects of her recovery, the secretary is making excellent progress and we are confident she will make a full recovery," they said in the statement.
"She is in good spirits, engaging with her doctors, her family and her staff," they said.
Doctors generally consider a thrombus to be normal in cases of injury.
Aides said earlier this month Clinton, 65, had become dehydrated because of a stomach virus she contracted while in Europe. She fainted when she was alone at home in Washington and struck her head, causing the concussion, they said.
They said the concussion was not diagnosed immediately.
As a result of her fall and concussion, Clinton did not testify before Congress Dec. 20 about the deadly Sept. 11 attack on the U.S. mission in Benghazi, Libya. She said in a letter to the heads of both panels Dec. 17 she would answer their questions in January.
She issued a statement praising Kerry.
Clinton is widely considered a top Democratic presidential contender in 2016.
Monday's statement from her doctors and spokesman did not indicate when Clinton, who canceled most of her public events in recent weeks, intended to return to work.
The department earlier said she planned to be back at work this week after the New Year's Day holiday. At least one farewell trip was expected in January or February, The Washington Post reported.
Clinton spent the holidays with her family last week after working from home in the Hudson Valley, north of New York City.
Daughter Chelsea Clinton, 32, appeared "shaken" outside NewYork-Presbyterian Hospital, where her mother was being treated, the New York Daily News reported.
The former first lady has a history of blood clots. In 1998, a clot was found behind her right knee, and she was treated with blood-thinning drugs.
"That was the most significant health scare I've ever had," she told the News in 2007.