In a statement, state officials said Clinton was discharged after her medical team advised her that she is making good progress on all fronts.
"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," an official said.
Doctors kept a close eye on Clinton while using blood thinners to break up a clot, located in a vein behind her right ear between her brain and skull. The 65-year-old had remained hospitalized since she was admitted to New York-Presbyterian Hospital on Sunday.
Doctors said Clinton was expected to make a full recovery from the blood clot. According to Clinton's spokesman Phillipe Reines, the clot formed while Clinton was battling a stomach virus and suffered a concussion during a fainting spell at her home in December.
In the meantime, her daughter Chelsea sent out an update on her mother's condition in a tweet thanking her followers for their thoughts, prayers, and heartfelt wishes.
"Thank you all for sending good thoughts my mom's way. Grateful to all her doctors and that she'll make a full recovery!" the tweet read.
This isn't the first time Clinton suffered a blood clot. In 1998, midway through her husband's second term as president, Clinton was in New York fundraising for the midterm elections when a swollen right foot led her doctor to diagnose a clot in her knee requiring immediate treatment.
The Associated Press contributed to this report.