Ms. Rice is set to meet the presidents of both nations in an effort to promote joint counter-terrorism efforts and democratic reforms.
Wednesday, she visited Afghanistan, where she praised recent elections for helping to open a new page in the nation's history.
Earlier this week, Ms. Rice met top officials in Kyrgyzstan and signed a deal allowing U.S. forces to continue using a key base to support operations in Afghanistan.
The Pentagon praised the agreement as a key part of U.S. efforts to stabilize Afghanistan and fight terrorism in the region.
Ms. Rice's trip does not include Uzbekistan, which has been criticized for its rejection of a probe into a government crackdown on an opposition rally in May.