"Her medical team advised her that she is making good progress on all fronts, and they are confident she will make a full recovery," Philippe Reines, deputy assistant secretary of state and Clinton spokesperson, said in a statement announcing her release Wednesday evening.
"She's eager to get back to the office, and we will keep you updated on her schedule as it becomes clearer in the coming days," he added.
Clinton walked out of New York Presbyterian Hospital accompanied by her husband, former President Bill Clinton, and daughter, Chelsea, for a brief period earlier Wednesday afternoon. The appearance led to speculation about her release, which was announced a couple of hours later.
Chelsea also tweeted about her mother's release from the hospital: "Grateful my Mom discharged from the hospital & is heading home. Even more grateful her medical team confident she'll make a full recovery."
Clinton had been admitted Sunday, after doctors found the clot during a medical test related to a concussion she suffered in December.
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She is being treated with blood thinners to dissolve the clot, which has not resulted in a stroke or any neurological damage. Doctors expect her to make a full recovery.
Earlier, State Department spokesperson Victoria Nuland told reporters in Washington that Clinton was in communication with aides and there was nothing new on her condition or treatment.
Clinton, 65, has not been publicly seen or heard from in more than three weeks since falling ill with severe stomach flu and a subsequent concussion that occurred when she fainted because of dehydration, officials said.
Asked how Clinton's illness might affect her plans to testify on Capitol Hill about the deadly 9/11 attack on the US diplomatic mission in Benghazi, Libya, Nuland did not directly say whether Clinton would appear.
"She has said that she is open to going up to the Hill. We are working with them now on their schedule because there's also a question of when they are going to be in and we will let you know when we have something to share," Nuland said.
Clinton, a former first lady, New York senator and presidential candidate, has said that she would quit once Senator John Kerry, President Barack Obama's choice as her successor, is confirmed by the Senate.
(Arun Kumar can be contacted at arun.kumar@ians.in)