He is now in isolation and is getting treatment from medical teams.
Save the Children say he is in the very best hands.
"He's just three years old, I would assume he is very scared and vulnerable at the moment," Save the Children's Alun McDonald said.
The Ugandan cases showed the epidemic was entering a "truly frightening" phase and was likely to spread further and kill many more people, one infectious disease specialist told Reuters.
"This epidemic is in a truly frightening phase and shows no sign of stopping anytime soon," said Jeremy Farrar, an infectious disease specialist and director of the Wellcome Trust global health charity which is involved in fighting Ebola.
The priority now will be to contain the virus and stop it from spreading further.
"We can expect and should plan for more cases in DRC and neighbouring countries," he said, adding: "There are now more deaths than any other Ebola outbreak in history, bar the West Africa Epidemic of 2013-16, and there can be no doubt that the situation could escalate towards those terrible levels."
Source: AAP/International Rescue Committee
The current Ebola epidemic began in August last year in eastern Congo and has already infected at least 2062 people, killing 1390 of them.
Until now Save the Children say the Ugandan ministry of health has done an excellent job of preventing the virus from reaching the country, "At the official border crossing there are screening points for Ebola that have been very effective. The ministry of health in Uganda has really been leading the efforts to prevent Ebola crossing, with great success."
Source: World Health Organization/AP
But the worry now is that health services in the area are already under pressure from the influx of refugees crossing in from the fighting in Eastern Congo, "This year alone we've had about 20 thousand Congolese refugees come into that area of Uganda. The health services in that area are very stretched at the moment, because of the refugee influx and now the risk of Ebola spreading as well."
Save the Children say efforts need to be stepped up to make sure the virus, which causes hemorrhagic fever with severe vomiting, diarrhoea and bleeding, won't spread.
"There's been a lot of work over the past year of informing communities about how to prevent Ebola, what to do if you start to see the symptoms and training rural health teams on what to do if there's a case."
The problem in the Democratic Republic of Congo according to aid agencies is that there's a lot of misinformation about Ebola spreading in communities. The inaccurate information has been a real challenge to bring the disease under control.
Children 'particularly vulnerable'
With two of the three cases in Uganda confirmed to be children, Save the Children say youngsters are at particular risk from the disease, "Ebola is one of those diseases that doesn't discriminate. In Congo, there have been hundreds of cases of children diagnosed and sadly, two of the three in Uganda so far," Mr McDonald from the agency said.
"It's passed through bodily contact, bodily fluids which can sometimes leave children particularly vulnerable, but it is a disease which affects whole families."
Even if children are not ill themselves, they can suffer because of the disease, "When family members are put into isolation for treatment, they're often left on their own, even if they're not affected themselves. There is a need for much greater support for the children of affected families."
This outbreak is the second largest on record after a West Africa epidemic in 2013-2016 infected 28,000 people and killed 11,300, mostly in Liberia, Guinea and Sierra Leone.
WHO due to hold an emergency committee
The World Health Organization said Wednesday that a key emergency committee would meet following confirmation that the virus has spread to Uganda.
The panel will meet on Friday to determine whether to declare the outbreak "a public health emergency of international concern," a major shift in the mobilisation against the disease, it said.
Until now, WHO's emergency committee had held off declaring the DRC epidemic an emergency of international concern, in part because the virus remained contained in one part of DRC.
For the committee to make the emergency call, it must determine that the epidemic "carries implications for public health beyond the affected State’s national border and may require immediate international action," according to WHO.