Mrs Clinton did not suffer a stroke or neurological damage as a result of the clot, the doctors said, adding "she is in good spirits, engaging with her doctors, her family and her staff".
Mrs Clinton, who has not been seen in public since December 7, was revealed on Sunday evening to be in a New York hospital having treatment for a blood clot that stemmed from a concussion she suffered in mid-December.
The concussion was itself the result of an earlier illness, described by the State Department as a stomach virus she had picked up during a trip to Europe that led to dehydration and a fainting spell after she returned to the US.
Mrs Clinton's doctors, in the statement released by the State Department, said: "In the course of a routine follow-up MRI on Sunday, the scan revealed 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.
"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."
Mrs Clinton's illness may raise questions about her fitness to be president should she make a new run for the White House in 2016. Barack Obama defeated her in the 2008 Democratic primary and then, upon his election as president, took the unusual step of tapping her for the most important post in his Cabinet.
Mrs Clinton earlier this month played down the notion she would run again for the White House in 2016, telling a TV interviewer: "I've said I really don't believe that that's something I will do again."
She is expected to step down when her replacement as secretary of state, Senator John Kerry, is confirmed by the Senate.