The Health ministry has confirmed a new Ebola case in Kasese district.
A girl of nine who had travelled from the neighbouring Democratic Republic of Congo was found to have a fever during screening for Ebola at the Mpondwe border crossing.
A blood sample that was sent for testing confirmed on Thursday evening that she had Ebola.
Initial symptoms can include a sudden fever, intense weakness, muscle pain and a sore throat.
Subsequent stages can bring vomiting, diarrhoea and – in some cases – both internal and external bleeding.
The girl has been isolated and transferred to an Ebola treatment unit.
Uganda has maintained largely successful screening centres along its border with DR Congo in an effort to keep out an outbreak that has killed close to 2,000 people in the last year.
In June, there were two Ebola cases in the country.
A Ugandan man and his Congolese wife lost two sons after their return from a trip to DR Congo to see relatives.