Clinton was to meet beleaguered Somali President Sheik Sharif Sheik Ahmed to underscore U.S. backing for his government and an undermanned African Union peacekeeping force supporting it.
"We want to support (Ahmed) as he tries to assert power over parts of Somalia that have been riven with conflict since 1992," she told a town hall meeting at the University of Nairobi ahead of the meeting.
Somalia has not had an effective government since 1991 and Ahmed's administration holds only a few blocks in Mogadishu, with support from the peacekeepers.
Clinton praised their efforts.
"They are trying to create areas that are conflict-free zones," Clinton said. "We have made clear we want to be supportive. We want to support the African intervention into Somalia."
Ahmed said this week that his meeting with Clinton presents a "golden chance" for his war-torn country, which has been plagued by the insurgency led by the Islamist al-Shabab militia.
The U.S. considers al-Shabab a terrorist organization and accuses it of harboring suspects in the 1998 bombing of the American embassies in Kenya and Tanzania.
A spokesman for the group said Wednesday in Somalia that any U.S. plan to assist Ahmed's government or the peacekeepers would not stop them from fighting.
"Any support America gives the government will not deter us from pursuing our path because we believe Allah and we always hope from him to give us the upper hand," Sheikh Ali Mohamud Rage told reporters in Mogadishu.
The top U.N. envoy says the country is at a "turning point" and in desperate need of international support, especially military equipment, training and money.
U.S. officials said Clinton is not expected to announce specifics of new assistance to the Somali government. But they said the Obama administration plans to go ahead with additional weapons supplies through African nations to double an initial provision of 40 tons of arms.
The U.S. also has begun a low-profile mission to help train Somali security forces in nearby Djibouti, said the officials, who spoke on condition of anonymity because of the sensitivities surrounding U.S. involvement in the program.
U.S. commanders still have sour memories of the 1992-94 American military intervention that began as a humanitarian mission to deliver aid supplies to Somalia.
It ended in a humiliating withdrawal months after the 1993 "Black Hawk Down" incident in which two U.S. helicopters were downed and 18 servicemen were killed.
Earlier Thursday, Clinton honored the victims of the 1998 embassy attacks in Nairobi and Dar es Salaam that killed more than 200 people.
A day before the 11th anniversary of the Aug. 7 bombings, she paid a somber visit to a memorial at the site of the former Nairobi embassy where 218 people died.
The site, she said, is a reminder of "the continuing threat of terrorism, which respects no boundaries, no race, ethnicity or religion, but is aimed at disrupting and denying the opportunity of people to make their own decisions and to lead their own lives."
Clinton placed a wreath at the site, signed a guestbook and met with survivors of the Nairobi bombing. She said it was a day "to renew our resolve to do all that we can to ensure that these attacks don't take more innocent lives in the future."
The top U.N. envoy for Somalia said last month that the country is at a "turning point" and in desperate need of international support, especially military equipment, training and money.