"The 15-year-old has finally died. He died yesterday," Dr Francis Karteh, head of Liberia's national Ebola crisis unit, told AFP.
He added that the teenager's parents had also tested positive for the virus and were under observation in the capital Monrovia.
It was confirmed last week that the boy and two of his relatives had contracted Ebola, which has left more than 11,300 people dead since December 2013 in its worst ever outbreak, mainly in the west African nations of Guinea, Liberia and Sierra Leone.
The World Health Organisation previously reported that the boy was 10 years old, but Karteh said he was in fact 15.
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He fell sick on November 14 and was hospitalised three days later in Monrovia, the WHO said, adding that 150 people who had been in contact with the family were being monitored.
Since the beginning of the outbreak, Liberia has registered more than 10,600 cases and more than 4,800 deaths, according to a WHO situation report published last week.
That announcement triggered a 42-day countdown -- twice the incubation period of the virus -- before Guinea can be declared Ebola-free.
Sierra Leone was declared to have beaten the virus earlier this month.