There has been a deadly outbreak of the virus in the neighbouring country, Democratic Republic of Congo. The virus has now spread to Uganda and the child's death is the first reported in Uganda.
Officials said the grandmother and younger brother of the deceased also have the disease.
The boy is said to have travelled across the border with his family from DR Congo on Sunday. He was taken to a Ugandan hospital when he began exhibiting symptoms, including vomiting blood, officials said.
More than 2,000 cases of Ebola have been recorded in DR Congo in the last 10 months, out of which most of them have ended in death.
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