Haley will meet with officials from the African Union in Addis Ababa on Monday before traveling on to Juba and Kinshasa for talks with leaders and to meet with UN peacekeepers, said a US statement.
Haley "will witness firsthand the UN operations working to address conflict and devastation in these countries, including visits with UN peacekeeping missions and sites of other UN agencies providing life-saving humanitarian aid," said the statement on Friday.
Trump told the African leaders he was "deeply disturbed by the ongoing violence in South Sudan and in the Congo" but said peace and prosperity would come through an African-led process.
Haley, he said, would discuss conflict resolution and "most importantly, prevention" during her trip.
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Nine months into his presidency, Trump has shown little interest in Africa and Haley's trip is a first opportunity for his administration to shape its policy toward the continent.
Haley's visit to South Sudan comes as regional leaders have launched a new peace initiative aimed at kick-starting the effort to end the nearly four-year war that has left tens of thousands dead and millions uprooted.
The United States is South Sudan's biggest aid provider and a key supporter of its 2011 independence from Sudan.
Last month, Haley told the Security Council that the regional effort was the "last chance" for peace in South Sudan and said leaders should get behind the initiative.
Elections were supposed to take place this year under a transitional deal aimed at avoiding bloodshed after President Joseph Kabila refused to step down when his second and final term ended in December 2016.
But the DR Congo's electoral commission is facing logistical hurdles and this month said it would need another 504 days to prepare for the vote, which means the elections would not be held before early 2019.
South Sudan and the DR Congo host two of the biggest and costliest UN peacekeeping missions.
Some 14,000 peacekeepers have been deployed to South Sudan and 18,000 blue helmets are tasked with protecting civilians in the DR Congo.
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