Trump told the African leaders he was “deeply disturbed by the ongoing violence in South Sudan and in the DRC” 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.
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.
The 45-year-old former governor of South Carolina has emerged as a leading voice on US foreign policy, at times outshining US Secretary of State Rex Tillerson.
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.
In the DRC, the United States has joined calls from the Security Council for Kinshasa to announce a date for elections in the vast resource-rich African country.
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 DRC’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 DRC host two of the biggest and costliest UN peacekeeping missions.
During negotiations this year, Haley was a driving force behind a $600m cut to the peacekeeping budget and has vowed to review each UN mission to look at further savings.
Some 14 000 peacekeepers have been deployed to South Sudan and 18 000 blue helmets are tasked with protecting civilians in the DRC.