In a statement, the Ugandan government said the patient who died was a Congolese citizen whose body had already been returned to DR Congo.
A laboratory has also confirmed an Ebola case in the eastern city of Goma, currently controlled by the M23 rebels, the AFP news agency reported on Sunday.
At least six Americans have been exposed to Ebola in DR Congo, and one has displayed symptoms but none have been confirmed to have been infected, the BBC's US partner CBS reports, citing sources.
The US government was reportedly trying to transport them out of the country, possibly to a military base in Germany, STAT News reports.
The US Centers for Disease Control and Prevention (CDC) said it planned to send more staff to DR Congo and Uganda, while the US Embassy in DR Congo issued a health alert reminding citizens not to travel to Ituri province.
The BBC has contacted the CDC for comment.
Jean Kaseya, director general of Africa Centres for Disease Control and Prevention, warned that in the absence of vaccines and effective medicines people should follow public health measures, including the guidance about handling the funerals of those who have died from the disease.
"We don't want people infected because of funerals," he told the BBC World Service's Newsday programme.
Community funerals, where people helped wash the bodies of their loved ones, contributed to many people becoming infected in the earlier stages of the big outbreak more than a decade ago.
The WHO said the ongoing security situation and humanitarian crisis in DR Congo, combined with high population mobility, the urban location of the hotspot, and the large number of informal healthcare facilities in the region increased the risk of spread.
Countries bordering the DR Congo are considered high risk due to trade and travel.
Rwanda said it would be tightening screening along the country's border with DR Congo as a "precautionary measure".
Its health ministry said surveillance systems had been strengthened and health teams were on alert to "ensure early detection and rapid response if needed".
Ebola was first discovered in 1976 in what is now DR Congo, and is thought to have spread from bats. This is the 17th outbreak of the deadly viral disease in the country.
There is no proven cure for Ebola, with the average fatality rate is around 50%, according to the WHO.
Africa CDC previously said it was concerned by the high risk of further spread due to the urban settings of Rwampara and Bunia, and mining activities in Mongwalu.
The health agency's executive director Dr Jean Kaseya added that "significant population movement" between the affected areas and neighbouring countries also meant regional co-ordination was essential.
Around 15,000 people have died from the virus in African countries over the past 50 years.
DR Congo's deadliest outbreak was between 2018 and 2020, during which nearly 2,300 people died.
Last year, 45 people died after an outbreak in a remote region.