The death brings the total number of fatalities in the country to two since Ghana registered its first ever outbreak of the disease last month.
The outbreak is only the second in West Africa. The first ever case of the virus in the region was detected last year in Guinea.
The virus is transmitted to people from fruit bats and spreads among humans through direct contact with bodily fluids, surfaces and materials, the WHO said.
The dead child, whose gender or age were not disclosed, was one of two new cases reported last week by WHO.
"Last week I mentioned the two additional cases. One is the wife of the index case and the other one is the child of the index case and the child unfortunately died, but the wife is still alive and improving," WHO doctor, Ibrahima Soce Fall said.
The Ghanaian health ministry has only reported three confirmed cases and further testing remains to be done on a fourth suspected case, Soce Fall said.
The first two cases, in southern Ghana's Ashanti region, both had symptoms including diarrhoea, fever, nausea and vomiting, before dying in hospital, the WHO said previously.
But one of those two cases was later declared a false-positive.
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