"The child and his family entered the country through Bwera Border post and sought medical care at Kagando hospital where health workers identified Ebola as a possible cause of illness," the WHO said in a statement issued on Tuesday.
This is the second largest Ebola outbreak in history. Over 1,300 people have lost their lives due to the virus since August. The main areas which have been severely affected are DR Congo's North Kivu and Ituri provinces.
A recent spike in the number of those found to be infected with Ebola has raised concerns about the spread of the virus across DR Congo's borders. In anticipation of this, health workers in Uganda have been vaccinated against it and trained to recognise symptoms of the infection.
"Although there have been numerous previous alerts, this is the first confirmed case in Uganda during the Ebola outbreak on-going in neighbouring Democratic Republic of the Congo," WHO said.
Around 11,000 people had lost their lives in the deadliest Ebola outbreak which occurred in 2014.
Ebola first appeared in 1976 in Sudan, followed by DR Congo. The virus can be transmitted to humans from wild animals. Symptoms of the disease include fever, severe headache and haemorrhaging.
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