The victim, a 50-year-old woman, was the grandmother of the five-year-old boy who died on Tuesday.
They had travelled to DRC with their family for the burial of a relative, who was believed to have been infected by the virus.
On Wednesday the health ministry said Uganda recorded three cases of Ebola infection, from the same familiy that travelled to DRC.
The third case is the boy's three-year-old brother.
The family has been quarantined in a hospital in Bwera, in Kasese district. Eight other people who had been in contact with them were also being monitored, and they are due to be vaccinated Friday with a new drug.
These are the first confirmed Ebola cases outside the DRC since an outbreak began there a year ago. More than 2,000 cases have been recorded in DRC, about two thirds of them fatal.