Mrs Clinton's doctors discovered the clot while performing a follow-up examination, her spokesman Philippe Reines said.
He would not elaborate on the location of the clot but said Mrs Clinton is being treated with anti-coagulants and would remain at New York-Presbyterian Hospital for at least the next 48 hours so doctors can monitor the medication.
"Her doctors will continue to assess her condition, including other issues associated with her concussion," Mr Reines said in a statement. "They will determine if any further action is required."
Mrs Clinton, 65, fell and suffered a concussion while at home alone in mid-December as she recovered from a stomach virus that left her severely dehydrated.
The seriousness of a blood clot "depends on where it is", said Dr Gholam Motamedi, a neurologist at Georgetown University Medical Centre who was not involved in Mrs Clinton's care.
Clots in the legs are a common risk after someone has been bedridden, as Mrs Clinton may have been for a time after her concussion. Those are "no big deal" and are treated with six months of blood thinners to allow them to dissolve on their own and to prevent further clots from forming, he said.
A clot in a lung or the brain is more serious. Lung clots, called pulmonary embolisms, can be deadly, and a clot in the brain can cause a stroke, Dr Motamedi said.
Keeping Mrs Clinton in the hospital for a few days could allow doctors to perform more tests to determine why the clot formed, and to rule out a heart problem or other condition that may have led to it, he said.