The 65-year-old Clinton was suffering from a stomach virus earlier this month when she fainted due to dehydration, causing the concussion. She had to spend the holidays with her family last week.
According to Philippe Reines, deputy assistant secretary of state, Clinton is expected to remain at New York Presbyterian Hospital for the next 48 hours so doctors can monitor her condition and treat her with anti-coagulants.
"Her doctors will continue to assess her condition, including other issues associated with her concussion," Reines said. "They will determine if any further action is required."
Reines, however, did not specify where the clot was discovered.
Clinton is all set to step down as secretary of state when President Barack Obama finishes his first term in Jan 21, 2013. She will be succeeded by Democratic Senator John Kerry.