She is to meet with Afghan President Hamid Karzai on Thursday and hopes to show the United States' commitment to Afghanistan, the State Department said.
Clinton is also expected to discuss the relationship between Afghanistan and Pakistan.
A day before, her trip to Tripoli was the first by a Cabinet-level American official since the ouster of longtime strongman Moammar Gadhafi.
Clinton landed under tight security in Libya, where forces loyal to the transitional government are still battling Gadhafi loyalists.
Those forces toppled Gadhafi's nearly 42-year-old government in August after six months of fighting and NATO airstrikes.
In Afghanistan, coalition forces are in the process of transferring security control to Afghan forces ahead of a U.S. drawdown set to be completed by the end of 2014.
The 33,000 additional American troops sent in last year are scheduled to fully depart the war-torn country by September of next year.
U.S. special envoy Marc Grossman has been in the region for the past two weeks, the State Department reported.
