Her medical team said she was making good progress, and were confident she would make a full recovery, said the state department.
It added in a statement that she was “eager to get back to the office”.
Hillary Clinton was earlier seen leaving New York-Presbyterian Hospital with her husband and daughter.
The state department said at the time she had not been discharged, but was merely travelling to another hospital building on the campus for further tests.
Hillary Clinton, 65, is due to stand down before President Barack Obama formally begins his second term in January.
Appointed secretary of state at the start of Barack Obama’s first term, in January 2009, her health has been under intense scrutiny because she is considered a strong candidate for the Democratic nomination for president should she decide to run in 2016.
The former first lady was taken to hospital on Sunday when the clot was discovered. She had suffered a concussion earlier in the month after falling in her home.
She had fainted after becoming dehydrated while battling a stomach ailment, aides have said.
Hillary Clinton is being treated with blood thinners to dissolve the clot.
During her stay in hospital she worked from her bed, speaking with staff and reviewing paperwork, US state department officials said.
Renowned for her grueling travel schedule, Hillary Clinton’s most recent foreign trip in December was to Dublin.
“She’s been quite active on the phone with all of us,” spokeswoman Victoria Nuland said.
The secretary of state is due to give evidence before a Congressional committee later this month in connection with the attack in September on the US consulate in the Libyan city of Benghazi.
The US ambassador to Libya and three American officials were killed in the incident.
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