Clinton met with Libyan President Mohamed Magariaf in conjunction with the U.N. General Assembly.
U.S. forces assisted in a NATO-led mission last year meant to protect civilians from attacks by forces loyal to Libyan leader Moammar Gadhafi. The civil war resulted in Gadhafi's death and the emergence of a new government in Tripoli.
In mid-September, an attack described by the White House as an act of terror left the U.S. ambassador to Libya and three members of his staff dead.
Clinton said during a press briefing with Magariaf said the United States was "proud" to stand by its people during the civil war.
"And we will continue to stand with you as you now write Libya's new future as a democracy that will give all of your people a chance to have a better future," she said.
Magariaf expressed his condolences for the death of U.S. Ambassador Christopher Stevens and his staff members. What happened in Benghazi, he said, wasn't a reflection of the sentiments of the Libyan people.
The Libyan government said several people had been arrested in connection to the Benghazi attack. Clinton said federal investigators were in Libya examining the incident.