The boy developed fever on February 11 and was admitted to hospital five days later, the Indonesian health ministry's head of animal-borne infectious disease control, Rita Kusriastuti, told AFP.
"He suffered shortness of breath and eventually died on February 21. Laboratory tests confirmed he died from the H5N1 virus," she added.
Concerns about avian influenza have risen in Asia since China in late December reported its first fatality from the H5N1 virus in 18 months.
Indonesia has been the hardest-hit by bird flu, with 150 deaths reported between 2003 and 2011, according to the World Health Organization.
The health ministry said on its website that 154 people had now died of bird flu in Indonesia since 2005.
The virus typically spreads from birds to humans through direct contact, but experts fear it could mutate into a form that is easily transmissible between humans, with the potential to kill millions in a pandemic.
-AFP/ck
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