A scan on Sunday had revealed “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,” the doctors said in a statement.
But, they added, Mrs Clinton “is making excellent progress and we are confident she will make a full recovery.”
Mrs Clinton, 65, fell ill earlier this month with a stomach bug that led to her fainting and suffering a concussion, but her office had insisted that she was recovering and the top US diplomat was expected back at her desk on Monday.
Mrs Clinton is being treated at New York Presbyterian Hospital.