On Thursday, health workers in Congo's town of Beni began vaccinating pregnant women who have passed the first trimester and are considered contacts of an Ebola case.
The boy's three-year-old brother has also been infected with the virus, AP reported. Health ministry spokesman Emmanuel Ainebyoona on Thursday confirmed the woman's death.
The Democratic Republic of the Congo has been dealing with an ongoing Ebola outbreak since August 2018; during that time, more than 2,000 cases of the disease have been confirmed, the majority of which were ultimately fatal.
The first cross-border cases in this Ebola outbreak, the second-deadliest in history, have prompted a World Health Organisation expert committee to meet on Friday to discuss whether to declare a global health emergency.
A health ministry official told AFP on condition of anonymity that the two victims had "attended the burial of an Ebola patient in Congo, but returned to Uganda".More news: Elon Musk: Tesla is not dealing with a demand problem
The 3-year-old has been confirmed to be infected with Ebola.
Uganda's health ministry said three people who are suspected to have Ebola and are not related to the family remain in isolation, with tests pending.
Twenty-seven people who came into contact with the deceased have been placed under observation, the World Health Organization said in a statement.
According to WHO, Uganda has already administered the Ebola vaccine to around 4700 health care workers across 165 medical facilities.
There are about 10,000 to 20,000 people estimated to be crossing over from DR Congo to Uganda using the border points in the districts of Kasese, Bundibugyo, Kabarole and Kisoro, among others.More news: Pelosi says she's 'done' with Trump after latest insults
Uganda, a neighboring country, is more stable and developed that the DRC and has been preparing for the disease's spread beyond the borders. The illness causes internal bleeding and is easily transmitted through contact with small amounts of bodily fluid. "There's no shaking of hands, people just wave at each other".
According to the WHO, Uganda has vaccinated almost 4,700 health workers in 165 facilities with an experimental drug created to protect them against the virus.
Monitoring and vaccination had been stepped up, but there had been "no panic reaction" so far to the cases there.
The WHO will hold an emergency meeting on Friday to determine whether to declare the outbreak "a public health emergency of worldwide concern" - a major shift in mobilisation against the disease.
Authorities have struggled to contain the disease partly because health workers have been attacked almost 200 times this year in conflict-hit eastern Congo, the epicenter of the outbreak.More news: Zion Williamson Suing Florida Marketing Firm