A high-ranking State Department official said Clinton would use the trip to Uganda -- the second stop on her 11-day tour of seven African nations -- to encourage President Yoweri Museveni to keep up the hunt for Joseph Kony, the leader of the bloody rebellion by the Lord's Resistance Army.
The US has 100 Special Forces troops on the ground in the region helping search for Kony, who is wanted by the International Criminal Court for war crimes and atrocities committed by the LRA.
"We have worked very closely with Uganda in our efforts to track down, to find and to take Joseph Kony and the LRA," the State Department official said, calling Uganda "one of our most important security partners in the region for the last five years".
"The Secretary will applaud and compliment President Museveni on his efforts and encourage President Museveni to stay on course in the fight against the LRA and Kony," the official added.
Clinton is scheduled to meet Museveni on Friday and visit a military base where she will be briefed on the hunt for Kony and efforts to stamp out the Shebab Islamist militants in Somalia.
She will also visit a health centre and address human rights activists.
The State Department official said Clinton would compliment Museveni for his role in the fight against AIDS but encourage him to open up more space for democracy.
During his increasingly autocratic quarter-century in power, one of the main feathers in Museveni's cap has been his progressive approach to combating AIDS. He spearheaded a campaign that reduced Uganda's prevalence rate from more than 20 percent to around seven percent.
But a leaked US diplomatic cable accused Museveni, who won re-election to a new term in February 2011, of "autocratic tendencies" that "could relegate Uganda to the list of unstable African nations".
Clinton will also bring up the issue of human rights, particularly for the often persecuted gay and lesbian communities, the official said.
Clinton on Friday is also due to travel to South Sudan, the world's newest nation. The country celebrated its first anniversary on July 9, and the United States played a major part in its birth.
She will meet with President Salva Kiir, whose government has yet to agree on its border with the rump state of Sudan and settle a crippling dispute on oil revenues.
The UN Security Council has given the two countries, which this year came close to all-out war, until Thursday to reach a peace deal or face sanctions.
"We are encouraging both sides, South Sudan and Sudan, to effectively negotiate the differences between them," the State Department official said.
"Both countries are in a downward economic spiral as a result of their political differences and as the result of the cut-off in oil.
"In addition to showing our continued support, the Secretary will express our continued concern about the lack of movement in the resolution of the key issues that divide the two countries."
On her return from South Sudan, Clinton will pass back through Uganda, which is also in the midst of dealing with an outbreak of Ebola -- one of the world's most virulent diseases -- that has already killed 15 people nationwide.
Clinton's tour, which started in Senegal with warm praise for newly elected President Macky Sall, is focused on the Obama administration's new Africa strategy of promoting development by stimulating economic growth, advancing peace and security and strengthening democracy.
Clinton has now visited 104 countries as secretary of state, more than any predecessor. She will also visit Kenya, Malawi and South Africa and finish her trip by attending the state funeral of Ghana's late president John Atta Mills on August 10.