The girl had traveled with her grandmother hundreds of kilometers by bus from Guinea via Mali's capital to the western town of Kayes, where she was diagnosed on Thursday. Health workers were scrambling to trace hundreds of potential contacts in a bid to prevent Ebola taking hold in Mali.
The worst Ebola outbreak on record has killed 4,900 people, mainly in nearby Liberia, Sierra Leone and Guinea. A global response to the epidemic is being rolled out but experts warn that tens of thousands more people are at risk.
In a statement on Friday night, Mali's government confirmed the death of the girl, who has not been identified.
"In this moment of sadness, the government would like to express its condolences to her family and reminds the population that maintain very strict hygiene rules remains the best way to contain this disease," it said.
Mali is the sixth West African nation to record a case of Ebola. Senegal and Nigeria have successfully contained outbreaks and has been declared free of the disease. Spain and the United States have had a few cases.
Diplomatic sources have expressed concern about the preparedness of Mali, one of the world's poorest countries, to contain an outbreak. Home to a large U.N. peacekeeping mission, the mostly Muslim country is still battling northern Islamist militants after a brief French-led war last year.
WHO said that an investigation into the girl's case revealed that she had already started showing symptoms - and was therefore contagious - before being taken to Kayes.
"WHO is treating the situation in Mali as an emergency," the U.N. health agency said in a statement.
"The child’s symptomatic state during the bus journey is especially concerning, as it presented multiple opportunities for exposures – including high-risk exposures - involving many people," it added.
The girl was seen by health workers on Oct. 20 in Kayes but was referred to another hospital the next day where she tested positive for typhoid but was also bleeding from her nose. It was not until Oct. 23 that she tested positive for Ebola, WHO said.
WHO said that 43 contacts had been identified and isolated but a second Malian health official, who asked not to be identified, told Reuters that authorities estimated that at least 300 people had been in contact with the infected child.
Hours before Mali confirmed the case on Thursday, WHO Assistant Director-General Keiji Fukuda said the agency had "reasonable confidence" that there was not widespread transmission of the Ebola virus into neighboring countries.
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