The patient was suspected of having the virus when he was first treated at a clinic in the eastern city of Gobabis on 16 May. He was later transferred to Windhoek Central Hospital, where he died on 18 May, the health ministry said in a statement.
Laboratory results confirmed he had CCHF, which is a tick-borne virus that can also transmit between humans by close contact with blood or bodily fluids. It has a fatality rate of between 10% and 40%, the World Health Organization says.
The government has activated health-emergency committees to prevent further transmission and is closely monitoring all contacts of the deceased in Gobabis and Windhoek, it said.
So far 27 contacts have been identified, of whom 24 are health workers, it said.
Endemic in Africa, the Balkans, the Middle East and some Asian countries, CCHF symptoms include fever, muscle ache, dizziness, light sensitivity and vomiting, and can lead to organ failure and internal bleeding. It was first detected in Crimea in 1944.
Recent outbreaks in Africa have been limited in scope. Senegal confirmed one case of the fever in April.
Namibia has recorded six CCHF outbreaks since 2016, with a total of three deaths, the health ministry said.
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