Clinton met with the country's new leaders and presented them with an aid package totaling $11 million.
The package includes medical care for wounded fighters and additional assistance to secure weaponry that many fear could fall into the hands of terrorists.
Clinton is the highest ranking official in the Obama administration to visit Libya since the uprising against Moammar Gadhafi began in February.
Clinton encouraged the country's unsteady new leadership to commit to a democratic future free of retribution, and acknowledged in unusually blunt terms that the United States would like to see Gadhafi dead.
Until now, the U.S. has generally avoided saying that Gadhafi should be killed.
Clinton said as long as a threat continues, NATO would continue to protect civilians. The U.S. is a key part of the NATO-led air campaign that helped drive Gadhafi out, but U.S. officials have repeatedly said no U.S. combat soldiers are in the country and that the U.S. is not directly helping in the search for Gadhafi.
The Associated Press contributed to this report.